2K8 R2 + Citrix Xenapp 6 - File issue

Hi,  I have just encountered an odd issue in Win 2008 server where I have set permissions at the directory level for specific groups to access files and sub folders. However, when a user runs a program that opens that file for edit, the rights inherited from the parent folder are stripped (except administrators) and their individual username is added explicitly.     Also, a lock appears on the file's icon.  When I re-add the group rights, the lock then goes away again, only to have the same thing happen all over again.

The folder is under Program Files(x86).  Thinking this was some odd Creater Owner setting issue, I went to the top level folder and removed the Creator Owner from being listed at the top level and applied to all sub files and folders.  The problem still persists.  I would like users who are running the software, which opens this file to continue to be able to modify it, but not to have it result in having any exclusivity to the file after it is edited.  

No more than one user can run the program that uses this file by the way and it is not associated with any locking mechanisms to prevent multiple users of the software.  (That is accomplished through different means)

Thanks,
Jeff

This server is running as a terminal server with Citrix Xenapp 6, which I have verified I am confident is NOT a contributor to this issue.