I have updated my patch for SimplyThreaded. While I spotted the runaway-quote bug last time, I didn't fix it as completely as I thought. Fixed now. This patch requires the URI::Escape Perl module, which you probably already have if you're running MT.
Also added a feature: when you click "Reply" your view drops down to the comment-leaving form, even if you're not logged in (in which case you see the invitation to log in or leave an anonymous comment). Past behavior had the app simply ignore your clicking of "Reply" if you weren't logged in. That isn't good UI response.
I'll let it run a few days and then contact the author. Please let me know if you encounter any comment-leaving anomalies.
I've also activated the comment email notifcication thingy, explaining the new checkbox you see when you leave comments now.