Jason
I have seen something similar to this, when doing a tape restore from one machine to another, 4.12 upgraded to 5.5 then restored to another 5.5. The restore appeared to finish in 10 minutes but never gave the Restore complete message even after waiting over 2 hours. I'm not sure of the full implications of doing so, but you can Reconfigure your server using the control Console. Answer No to the Stop using the Server question (or similar) log in to the actual server as admin and then do Configure this server, You may need to change one of the settings so that the new config will be saved at the end. Then when it is up and working again just change the setting back again by repeating the Configure process.
Regards
Ray Mitchell