Thanks for posting, and sorry you're having trouble.
Often, an invisible difference can be caused by extended properties- if you tick the option to ignore these, do the tables get seen as identical?
If that doesn't help, it may well be to do with the schema difference you mentioned, in which case we will need to replicate the problem here. Could you do a Snapshot of the DB (from the File menu in Compare) and also zip up the scripts, then send those over to email@example.com
? Please quote F0060535 in the subject line.