File and directory permissions

We are running OSX 10.7 Lion on a Mac Pro 1,1 IN RAID. We are using this system als fileserver. Since last year it came to our attention that there where problems with the permissions on the files and directories (they seem corrupted). I do not mean system files but the files we stored on this server. When I look at random file permissions I get a whole list of users etc. A lot of duplicate users are there and also there are some entries in the list saying 'fetching'.

We use the server admin tool to manage groups and users.

This is what we have done so far:

- Try to repair permissions through terminal (because of RAID configuration)

- Propogate permissions through server app

- Resetpassword trick (restart cmd+R / terminal / resetpassword)

Can anyone tell me how to get this working 'clean' again? is there a way to reset all files according to the workgroup/user settings in the server app?