Hi,
I don't really know a lot about this but I've been seeing the same thing and I'm wondering how exactly Mozilla determines these threads. Does it use the subject line or the "In-Reply-To: <message-identifier>" header (also). As far as I can see the latter could at least be causing some of the errors you've mentioned, in which case it's not really a bug but actually caused by user behaviour.
Regards,
Steffan Jacobs.
