Unfortunately SQL Source Control behaves in this manner because full text indexes can't be updated transactionally, so we do them all at the end of the script, after the transaction. Unfortunately that means that if you have something which relies on them in the middle of the script, then it will fail.
The workaround is to synchronize the fulltext catalogs / tables with fulltext indexes first, and then synchronize the rest of the database.
There is a existing feature request you may want to vote for
http://redgate.uservoice.com/forums/390 ... ss-to-fail
These forums allow our users to request features and vote on them.
The development team actively monitor these forums so if a request receives alot of support the request maybe added to a future release.