Group Policy problem (Not Applied (Unknown Reason)

Few day ago we had problem with DFSR and errors (5014,4612,5002) due unclean shutdown. This has been solved now, SYSVOL is now synced. But now i have problems with User Preferences which are not applied.

We have lot of GPOs mostly computer policies and they we working ok. User policies are working also ok but preferences are not:

The following GPOs were not applied because they were filtered out
-------------------------------------------------------------------
    Local Group Policy
        Filtering:  Not Applied (Empty)

    Shortcutxxx
        Filtering:  Not Applied (Unknown Reason)

The user is a part of the following security groups

- User preferences are linked to the user OU and contain only User preferences (Shortcuts).

- Security Filtering is setup by Groups

After spending two day investigating i have noticed:

- When Security Filtering is setup by User or Group it does NOT work

- When Security Filtering is setup by authenticated user (bulid in) it does WORK.

Something is wrong with sec. filtering. No matter what policy is checked for user or group it DOES not work (Filtering:  Not Applied (Unknown Reason))

Groups or Users have right to read and apply GPO!

Please Help.

This all was working until yesterday, after DFSRs errors we fixed this does not work anymore.And if i set GPI to Group or User, on computer when i do :

gpupdate /force

and then

gupudate /r

i do not see this (Not Applied (Unknown Reason), i do not filtering at all (for this GPO). I must set Auth. users so policy apply and then set for user or group then i can see this. It is strange.

In basic, whatever policy if filtered by user or group, is NOT applied. or ((Not Applied (Unknown Reason)

Edit: To be clear. :

- create GPO, set sec. filtering to user or group and remove authe. user. Login to computer with that user and use :

gpresult /r

No policy.

- reate GPO, set sec. filtering to authe. user  Login to computer with that user and use same as above, and works. After that on DC change filtering to user or group and remove auth, go to pc and run:

gpupdate /force
gpresult /r

and got code:

Group Policy problem (Not Applied (Unknown Reason)