When logging into console or expanding the tree in Query and Report Designer you receive this error message in the login screen:
Internal error: Missing object in loaded collection
Delete local cache files for the console solved the problem.
Console cache location: C:\Documents and Settings\<user-name>\Local Settings\Application Data\Touchpaper On 2008 server and vista the files can be found under C:\Users\Default User\AppData\Local\Touchpaper
If this doesn't help then considering running the MDM (the utility you run to upgrade a Service Desk database) against the affected DB. Please ensure that you take a backup of the DB and have no one logged into the database before running the MDM.