I was doing a SBS 2003 to SBS 2008 migration and came across the fairly common journal wrap error. I fixed it using http://support.microsoft.com/kb/290762/en-us but the error still showed up in the Best Practise Analyser and when I tried to run the migration preparation tool it would not let me continue until I cleared the journal wrap errors.... after two server reboot there were no journal wrap errors in the event log but I still got the journal wrap warning in the migration tool. The answer was to clear the File Replication Log. Once that is clear the migration tool will finish successfully.
This also applies to the best practise analyser. Once the logs are cleared the best practise analyser will not show the journal wrap errors....assuming you have fixed them
