[Brian]

Sorry for the confusion here - I think Lizard misunderstood the error message you're getting. "Ignoring tail which cannot reach a root" is a different error than the one that the repair database script is meant to fix.

The script is giving you that message when it runs because your database isn't broken in the manner it expects, so it can't do anything.

The console messages you're getting are indeed caused by some files leftover from some long-fixed bugs from the beta. The files they're referring to are harmless to your data, but if they annoy you or you want to get your disk space back, the solution is to use
File -> Back Up Database...
and then use
File -> Revert to Database Backup...
choosing to revert to the backup you just made. That eliminates the disconnected transaction files from your database.

The sync problems are probably unrelated to the above, so I'll respond directly to the email you sent in so we can get that sorted out.