Odd Win7 connex issue (WinSCP, puTTY, FTP command line)

Question

I have searched in many forums and Google and have not seen anyone else mention this issue. So I hope I just missed it and someone can help. This issue I am encountering is this:

Whether I use WinSCP, puTTY or FTP in Windows CMD (command line), the first time I try and connect, it fails, but if I re-run the same command line or GUI setup, it will connect to my UUT (Unit Under Test). And this odd sequence will continue in an odd/even way. Meaning, if I close the successful (2nd try) and try a 3rd time (with the exact same command line or program setup) it will fail. But when I re-run the 4th time (same commands) it will connect. And on and on.

My setup is: I am using a PC with Win7 and connecting to a UUT (Unit Under Test) running Linux, on a closed network (not connected to the internet) through a Ethernet hub. All Firewalls are turned off (this is a test bench setup and not connected to the internet or any other computer network). I do not know if this occurs on any other Windows OS like XP.

My goal is to run some batch files to automate an FTP sequence, then put some files on the UUT. I also use puTTY to Telnet in and run test scripts on the UUT. I have successfully run some batch files but only in this strange fail/pass/fail/pass way.

This is an example of my code:

{{File upload_patch.bat}}
@ECHO OFF
cd\Users\lab\Desktop\
ftp -s:ftp.txt
call plink.bat
PAUSE

{{{File ftp.txt}}}
open 172.21.100.101
user
password
cd /
mkdir temp
cd /temp
lcd C:\SVDU-3W_Test\patch
mput svdu3*.*
y
y
quit

{{{{File ftp.txt}}}}
@ECHO OFF
cd\Users\lab\Desktop\
plink.exe user@172.21.100.101 -pw password chmod 755 /temp/svdu3*e
plink.exe user@172.21.100.101 -pw password PATH=$PATH:/bin;
/temp/svdu3_BIOS_recovery_util.sh