What causes the files in Program Files to be inaccessible?

Question

I have got strange problems on my notebook for months. I finally tracked down the problem to unusual situation in C:\Program Files, so now I ask this question here.

I have got two user accounts - HOME and WORK - both have got administrator privileges. Guest and built-in admin accounts are disabled. Whenever I install some software using HOME account, the other account can't use it. I tracked down the problems to inaccessible files in Program Files folder. ACL permissions are set correctly (Users group can read, Administrators group has got full access), compression and encryption is turned off. When I reboot to safe mode, the files are still accessible just by their creator (HOME user) and inaccessible from the other account. I can see all files, I can rename or move them, but can't read the contents. They seem like encrypted on NTFS level, but encryption flag is not set.

I have found this workaround: Login as HOME, pack all problem files into ZIP archive. Then logout. Then login as WORK, delete all those inaccessible files and unpack from ZIP. Now all works perfectly for all users, but only until some software tries to update itself using HOME user.

Additional information:

• Only some files are inaccessible, very often EXE and DLL ones, but it's not a rule. Other files are accessible normally.
• Inaccessible files are always created by HOME user, and all other users can't read them.
• File permissions of those inaccessible files can be managed by other administrator users, but regardless of permissions granted, they can never read the contents of those files.
• Owner of those inaccessible files is listed as Administrators group. Any administrator user can take the ownership of any file, but still can't read its contents.
• The system also refuses to create new user profiles, so I can't delete and recreate HOME user. (I can create new user accounts, but can't login to them. The Windows says it is unable to create the user profile for the new user. I expect it is due some problems in C:\Users, but I can't see any problems in there.)
• The file permissions (ACL settings) are identical to other computers I use. And all other computers work perfectly.
• chkdsk says there are no problems on C:
• It seems that D: volume doesn't exhibit these problems at all. (Not sure, but I have never had problems to access files on D:.) C: and D: are on the same physical drive.
• I don't know whether C:\Windows also have got the same problems, but Windows itself seems to work without problems.

Summary: From my point of view most probable cause of this strange behavior is NTFS file encryption. But encryption flag is not set. So my question is: What else can cause the files to be inaccesible by other users, even in Windows safe mode?