DomainServer-01 (Main DC, has all the roles etc...) Runs Server 2008 - Is a Virtual Server
FileServer (Backup DC, no roles) Runs Server 2003 - Is a Physical Server
The HDD in the Hyper-V Server which runs the Virtual Servers Failed and as such, the Virtual DomainServer-01 went offline for 2 days. The FileServer took over for those 2 days and people were still able to log on.
The Virtual DomainServer-01 has now been moved to a new physical host and started up - at first it looked like everything was OK, but I've noticed alot of people are not having the group policies applied to them, and as such, are not having the logon scripts run so no drives are mapped or printers are installed.
I've taken some screenshots to try and show what the results are of performing certain actions, it looks like the FileServer cannot connect to DomainServer-01 and so when a computer starts up, it's a luck of the draw which DC it connects to.
I've tried restarting both DCs but that doesn't seem to have solved any of the problems.
Are you restoring your DC from a snapshot by any chance?
we had a horrible time restoring a DC from a snapshot. In the end we just seized the rolls and built/introduced a new DC.
Later on I discovered you should not be doing snapshots for DC's, unless your snapshots are taken within 5 mins of each other (or some such). Could be wrong though. This is one of the reasons even M$ recommend not virtualising DC's
They used to not recommend virtualising DCs, but that's not the case now - we're going to be virtualising our DCs this summer.
However, they do say DON'T snapshot DCs as you'll get just the problems the OP mentioned
I discovered that I had this issue today, after a slight knock out yesterday.
Check your event logs for NTFRS issues, use the event log number to search for resolutions. this sorted my issue out. If you do find any NTFRS warnings/errors, and need any pointers, post and I'll see if they're the same as mine. If nothing simple comes up from the searches, then rebuild would be the best solution.