What version of the API do you have there? Early versions of v6 had a couple of problems when saving certain databases to scripts, which would end up with them writing out a 'dbo' and a 'DBO' schema, causing the error you're seeing, and previous versions have had similar problems synchronizing 2000 and 2005 databases.
If you're using 126.96.36.1991 and it's still doing this, I'd like to know more details about exactly what you're doing, so I can track down where the probelm's coming from. e.g. what are the database verisons / types on each side, where in the code is the exception thrown, if possible the code you're using / full stack trace / backups or snapshots or folders with the databases in (to email@example.com
for things you don't want to post publically).