Threads are linked based on the references header information. The usual cause of bad threading is some id10t that select an old email, presses reply and then deletes the subject and contents, blissfully unaware that there is more to an email that what they can see. The cure is teaching your correspondents to create new emails instead of trying to reuse old ones.

This is pretty much what I figured, but does not always seem to be the case. Furthermore, I can't retrain everyone I correspond with, so an operational solution within Thunderbird would be much appreciated.