The culprit is usually the insane Windows ACL permission system. Unix permissions look like "rwxr-xr-x" while a very simple example of a Windows permission is:
D:(A;OICI;FA;;;SY)(A;OICI;FA;;;WD)
Windows is a single user OS. If you are depending on its local user permission access control to be anything more than advisory you are going to have a bad time.