Thank you Plamen, I have thought of doing the conversion in several runs, but then I would have to do a robocopy or something similar in order to synchronize everything in the end. I would prefer having the synchronization option available since these tasks will be running over quite a few days.
Regarding the registry error, this happens to not only these 3 W2K8 R2 file servers, but also another windows 2003 server. In my opinion it would be highly unlikely that all of these would have registry errors.
The worker service runs fine and nothing's crashed according to windows event logs etc. Everything looks fine really. Except for the failing jobs of course 