server running server 2012 R2 - clients running server 2012 R2 and windows 8.1 pro

I have several GPOs linked to the domain root, some have user configurations only and some have computer configurations only. The problem is that:

1. Settings are not interfered between the GPOs
2. Only GPOs with user configurations are applied when I run `gpresult
/r` from a test machine!!

I have tried enabling processing loop back and then disabled it, with no results!

I know I am missing something, any help?