For some reason, after upgrading to the Samba version from Lenny-backports I needed to support Windows 7 profiles, the workstations suffered from severe problems. The entire profile seemed to be read-only, even though they weren’t on disk. I couldn’t change any setting and reverting profile configuration from backups didn’t help. In the end, the only thing that fixed it was recreating the user profile, both server and client side. This was an upgrade from 3.2.5 to 3.4.7.
Another issue I had is that the user database got a new backend and all the users were gone. You can import your existing smbpasswd file with pdbedit.
So, when doing this again, be sure to make workstation and server backups.