Cygwin Openssh key authentication doesn't work in Windows environment

Question

I use Unison on a Windows 10 machine to backup my files to a remote server running CentOS. I connect to the remote machine without a password using OpenSSH and public keys in Cygwin. I have never had any problems until recently.

If I connect to the remote machine using ssh user@remoteaddress within the Cygwin shell I have no problems and the keys work. If I try exactly the same command within the Windows command prompt the connection asks for my password.

This all started after I modified my Cygwin installation. However I tried re-installing Cygwin and generating new keys but get the same result.

All the threads I have found on this subject suggest checking your file permissions for the .ssh directory on the server and local machine. However this does not explain why it works within Cygwin but not within Windows and nothing on the server has changed.

I have added Cygwin to the Windows environment path correctly and ssh is recognized within the command prompt. It feels like OpenSSH or Cygwin has been updated and the update has broken the integration with Windows.

I'm not a programmer so this is beyond my ability at the moment.

Here are the logs from the command prompt and following that the logs from the Cygwin shell:

Microsoft Windows [Version 10.0.10586]
(c) 2015 Microsoft Corporation. All rights reserved.

C:\Users\myname>ssh -vvv [e-mail]
OpenSSH_5.4p1, OpenSSL 1.0.0 29 Mar 2010
debug1: Reading configuration data /etc/ssh/ssh_config
debug2: ssh_connect: needpriv 0
debug1: Connecting to myname.net [xx.xx.xxx.xxx] port 22.
debug1: Connection established.
debug1: identity file /.ssh/id_rsa type -1
debug1: identity file /.ssh/id_rsa-cert type -1
debug1: identity file /.ssh/id_dsa type -1
debug1: identity file /.ssh/id_dsa-cert type -1
debug1: Remote protocol version 2.0, remote software version OpenSSH_5.3
debug1: match: OpenSSH_5.3 pat OpenSSH*
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_5.4
debug2: fd 3 setting O_NONBLOCK
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug2: kex_parse_kexinit: diffie-hellman-group-exchange-sha256,diffie-hellman-group-exchange-sha1,diffie-hellman-group14-sha1,diffie-hellman-group1-sha1
debug2: kex_parse_kexinit: [e-mail],[e-mail],ssh-rsa,ssh-dss
debug2: kex_parse_kexinit: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,[e-mail]
debug2: kex_parse_kexinit: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,[e-mail]
debug2: kex_parse_kexinit: hmac-md5,hmac-sha1,[e-mail],hmac-ripemd160,[e-mail],hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: hmac-md5,hmac-sha1,[e-mail],hmac-ripemd160,[e-mail],hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: none,[e-mail],zlib
debug2: kex_parse_kexinit: none,[e-mail],zlib
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit: first_kex_follows 0
debug2: kex_parse_kexinit: reserved 0
debug2: kex_parse_kexinit: diffie-hellman-group-exchange-sha256,diffie-hellman-group-exchange-sha1,diffie-hellman-group14-sha1,diffie-hellman-group1-sha1
debug2: kex_parse_kexinit: ssh-rsa,ssh-dss
debug2: kex_parse_kexinit: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,[e-mail]
debug2: kex_parse_kexinit: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,[e-mail]
debug2: kex_parse_kexinit: hmac-md5,hmac-sha1,[e-mail],hmac-sha2-256,hmac-sha2-512,hmac-ripemd160,[e-mail],hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: hmac-md5,hmac-sha1,[e-mail],hmac-sha2-256,hmac-sha2-512,hmac-ripemd160,[e-mail],hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: none,[e-mail]
debug2: kex_parse_kexinit: none,[e-mail]
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit: first_kex_follows 0
debug2: kex_parse_kexinit: reserved 0
debug2: mac_setup: found hmac-md5
debug1: kex: server->client aes128-ctr hmac-md5 none
debug2: mac_setup: found hmac-md5
debug1: kex: client->server aes128-ctr hmac-md5 none
debug1: SSH2_MSG_KEX_DH_GEX_REQUEST(1024<1024<8192) sent
debug1: expecting SSH2_MSG_KEX_DH_GEX_GROUP
debug2: dh_gen_key: priv key bits set: 123/256
debug2: bits set: 521/1024
debug1: SSH2_MSG_KEX_DH_GEX_INIT sent
debug1: expecting SSH2_MSG_KEX_DH_GEX_REPLY
debug3: check_host_in_hostfile: host myname.net filename /.ssh/known_hosts
debug3: check_host_in_hostfile: host myname.net filename /.ssh/known_hosts
debug3: check_host_in_hostfile: match line 2
debug3: check_host_in_hostfile: host xx.xx.xxx.xxx filename /.ssh/known_hosts
debug3: check_host_in_hostfile: host xx.xx.xxx.xxx filename /.ssh/known_hosts
debug3: check_host_in_hostfile: match line 1
debug1: Host 'myname.net' is known and matches the RSA host key.
debug1: Found key in /.ssh/known_hosts:2
debug2: bits set: 486/1024
debug1: ssh_rsa_verify: signature correct
debug2: kex_derive_keys
debug2: set_newkeys: mode 1
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug2: set_newkeys: mode 0
debug1: SSH2_MSG_NEWKEYS received
debug1: Roaming not allowed by server
debug1: SSH2_MSG_SERVICE_REQUEST sent
debug2: service_accept: ssh-userauth
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug2: key: /.ssh/id_rsa (0x0)
debug2: key: /.ssh/id_dsa (0x0)
debug1: Authentications that can continue: publickey,gssapi-keyex,gssapi-with-mic,password
debug3: start over, passed a different list publickey,gssapi-keyex,gssapi-with-mic,password
debug3: preferred publickey,keyboard-interactive,password
debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive,password
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Trying private key: /.ssh/id_rsa
debug3: no such identity: /.ssh/id_rsa
debug1: Trying private key: /.ssh/id_dsa
debug3: no such identity: /.ssh/id_dsa
debug2: we did not send a packet, disable method
debug3: authmethod_lookup password
debug3: remaining preferred: ,password
debug3: authmethod_is_enabled password
debug1: Next authentication method: password
[e-mail]'s password:

...and from Cygwin shell :

myname@Windoze ~
$ ssh -vvv [e-mail]
OpenSSH_7.1p1, OpenSSL 1.0.2e 3 Dec 2015
debug1: Reading configuration data /etc/ssh_config
debug2: ssh_connect: needpriv 0
debug1: Connecting to myname.net [xx.xx.xxx.xxx] port 22.
debug1: Connection established.
debug1: identity file /home/myname/.ssh/id_rsa type 1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_rsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_dsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_dsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_ecdsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_ecdsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_ed25519 type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/myname/.ssh/id_ed25519-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_7.1
debug1: Remote protocol version 2.0, remote software version OpenSSH_5.3
debug1: match: OpenSSH_5.3 pat OpenSSH_5* compat 0x0c000000
debug2: fd 3 setting O_NONBLOCK
debug1: Authenticating to myname.net:22 as 'myname'
debug3: hostkeys_foreach: reading file "/home/myname/.ssh/known_hosts"
debug3: record_hostkey: found key type RSA in file /home/myname/.ssh/know                                                                        n_hosts:1
debug3: load_hostkeys: loaded 1 keys from myname.net
debug3: order_hostkeyalgs: prefer hostkeyalgs: [e-mail],ssh-                                                                        rsa
debug1: SSH2_MSG_KEXINIT sent
debug1: SSH2_MSG_KEXINIT received
debug2: kex_parse_kexinit: [e-mail],ecdh-sha2-nistp256,ecdh-                                                                        sha2-nistp384,ecdh-sha2-nistp521,diffie-hellman-group-exchange-sha256,diffie-hel                                                                        lman-group-exchange-sha1,diffie-hellman-group14-sha1
debug2: kex_parse_kexinit: [e-mail],ssh-rsa,ecdsa-sha2-nistp                                                                        [e-mail],[e-mail],ecdsa-sha2-nis                                                                        [e-mail],[e-mail],ecdsa-sha2-nistp256,                                                                        ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,ssh-ed25519
debug2: kex_parse_kexinit: [e-mail],aes128-ctr,aes192-ctr,a                                                                        es256-ctr,[e-mail],[e-mail],arcfour256,arcfour128,ae                                                                        s128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,rijndae                                                                        [e-mail]
debug2: kex_parse_kexinit: [e-mail],aes128-ctr,aes192-ctr,a                                                                        es256-ctr,[e-mail],[e-mail],arcfour256,arcfour128,ae                                                                        s128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,rijndae                                                                        [e-mail]
debug2: kex_parse_kexinit: [e-mail],[e-mail],hmac                                                                        [e-mail],[e-mail],[e-mail]                                                                        m,[e-mail],[e-mail],hmac-sha2-256,hmac-sha2-512,hmac-sha1                                                                        ,[e-mail],[e-mail],hmac-sha1-96-etm@openss                                                                        h.com,[e-mail],hmac-md5,hmac-ripemd160,hmac-ripemd160@openssh                                                                        .com,hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: [e-mail],[e-mail],hmac                                                                        [e-mail],[e-mail],[e-mail]                                                                        m,[e-mail],[e-mail],hmac-sha2-256,hmac-sha2-512,hmac-sha1                                                                        ,[e-mail],[e-mail],hmac-sha1-96-etm@openss                                                                        h.com,[e-mail],hmac-md5,hmac-ripemd160,hmac-ripemd160@openssh                                                                        .com,hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: none,[e-mail],zlib
debug2: kex_parse_kexinit: none,[e-mail],zlib
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit: first_kex_follows 0
debug2: kex_parse_kexinit: reserved 0
debug2: kex_parse_kexinit: diffie-hellman-group-exchange-sha256,diffie-hellman-g                                                                        roup-exchange-sha1,diffie-hellman-group14-sha1,diffie-hellman-group1-sha1
debug2: kex_parse_kexinit: ssh-rsa,ssh-dss
debug2: kex_parse_kexinit: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour12                                                                        8,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,rij                                                                        [e-mail]
debug2: kex_parse_kexinit: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour12                                                                        8,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,rij                                                                        [e-mail]
debug2: kex_parse_kexinit: hmac-md5,hmac-sha1,[e-mail],hmac-sha2-256,                                                                        hmac-sha2-512,hmac-ripemd160,[e-mail],hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: hmac-md5,hmac-sha1,[e-mail],hmac-sha2-256,                                                                        hmac-sha2-512,hmac-ripemd160,[e-mail],hmac-sha1-96,hmac-md5-96
debug2: kex_parse_kexinit: none,[e-mail]
debug2: kex_parse_kexinit: none,[e-mail]
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit:
debug2: kex_parse_kexinit: first_kex_follows 0
debug2: kex_parse_kexinit: reserved 0
debug1: kex: server->client aes128-ctr [e-mail] none
debug1: kex: client->server aes128-ctr [e-mail] none
debug1: SSH2_MSG_KEX_DH_GEX_REQUEST(1024<3072<8192) sent
debug1: got SSH2_MSG_KEX_DH_GEX_GROUP
debug2: bits set: 1579/3072
debug1: SSH2_MSG_KEX_DH_GEX_INIT sent
debug1: got SSH2_MSG_KEX_DH_GEX_REPLY
debug1: Server host key: ssh-rsa SHA256:1vQHO4ohl/PU9lJtFh8OVhQv0vdILmzJ4/AXdYt6                                                                        208
debug3: hostkeys_foreach: reading file "/home/myname/.ssh/known_hosts"
debug3: record_hostkey: found key type RSA in file /home/myname/.ssh/know                                                                        n_hosts:1
debug3: load_hostkeys: loaded 1 keys from myname.net
debug3: hostkeys_foreach: reading file "/home/myname/.ssh/known_hosts"
debug3: record_hostkey: found key type RSA in file /home/myname/.ssh/know                                                                        n_hosts:1
debug3: load_hostkeys: loaded 1 keys from xx.xx.xxx.xxx
debug1: Host 'myname.net' is known and matches the RSA host key.
debug1: Found key in /home/myname/.ssh/known_hosts:1
debug2: bits set: 1524/3072
debug2: set_newkeys: mode 1
debug1: SSH2_MSG_NEWKEYS sent
debug1: expecting SSH2_MSG_NEWKEYS
debug2: set_newkeys: mode 0
debug1: SSH2_MSG_NEWKEYS received
debug1: Roaming not allowed by server
debug1: SSH2_MSG_SERVICE_REQUEST sent
debug2: service_accept: ssh-userauth
debug1: SSH2_MSG_SERVICE_ACCEPT received
debug2: key: /home/myname/.ssh/id_rsa (0x60006bcf0),
debug2: key: /home/myname/.ssh/id_dsa (0x0),
debug2: key: /home/myname/.ssh/id_ecdsa (0x0),
debug2: key: /home/myname/.ssh/id_ed25519 (0x0),
debug1: Authentications that can continue: publickey,gssapi-keyex,gssapi-with-mi                                                                        c,password
debug3: start over, passed a different list publickey,gssapi-keyex,gssapi-with-m                                                                        ic,password
debug3: preferred publickey,keyboard-interactive,password

debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive,password
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Offering RSA public key: /home/myname/.ssh/id_rsa
debug3: send_pubkey_test
debug2: we sent a publickey packet, wait for reply
debug1: Server accepts key: pkalg ssh-rsa blen 279
debug2: input_userauth_pk_ok: fp SHA256:bBS6l5Dl4OBi2MHpBjSxJmRHXg6Q5g3+PMKvHKNm                                                                        CZM
debug3: sign_and_send_pubkey: RSA SHA256:bBS6l5Dl4OBi2MHpBjSxJmRHXg6Q5g3+PMKvHKN                                                                        mCZM
debug1: Authentication succeeded (publickey).
Authenticated to myname.net ([xx.xx.xxx.xxx]:22).
debug1: channel 0: new [client-session]
debug3: ssh_session2_open: channel_new: 0
debug2: channel 0: send open
debug1: Requesting [e-mail]
debug1: Entering interactive session.
debug2: callback start
debug2: fd 3 setting TCP_NODELAY
debug3: ssh_packet_set_tos: set IP_TOS 0x10
debug2: client_session2_setup: id 0
debug2: channel 0: request pty-req confirm 1
debug2: channel 0: request shell confirm 1
debug2: callback done
debug2: channel 0: open confirm rwindow 0 rmax 32768
debug2: channel_input_status_confirm: type 99 id 0
debug2: PTY allocation request accepted on channel 0
debug2: channel 0: rcvd adjust 2097152
debug2: channel_input_status_confirm: type 99 id 0
debug2: shell request accepted on channel 0
Last login: Sun Dec 20 08:34:02 2015 from ebradford.plus.com
[myname@mynameserver ~]$ debug2: client_check_window_change: changed
debug2: channel 0: request window-change confirm 0
[myname@mynameserver ~]$ ^C

Answer 1

SSH from MS Shell is even different version than the one from Cygwin:

OpenSSH_5.4p1, OpenSSL 1.0.0 29 Mar 2010 (MS)
OpenSSH_7.1p1, OpenSSL 1.0.2e 3 Dec 2015 (cygwin)

You see the obvious difference between Cygwin:

debug1: identity file /home/myname/.ssh/id_rsa type 1

and MS:

debug1: identity file /.ssh/id_rsa type -1

MS version is searching for key pair in some nonsense path and does not find it. You probably need to try from windows shell like this:

$ ssh -i /path/to/your/id_rsa [e-mail]