Thanks for your post.
I've seen this behavior from SQL Source Control when there's some reason it isn't correctly scripting objects. What happens is it puts the incorrect script in your repository, but at the next commit, it can't find it in the repository and assumes it's not there and that you have to commit again.
Can you check in your repository in the tables folder for the script associated with your table? I'm guessing you won't see the DISABLE TRIGGER statement in there. (If that's the case, you might be able to "fix" the problem by manually adding it into the script, then unlinking and relinking your database.)
I'm also happy to work with you on the phone or through the ticket we have open for you (ticket #16799).