I am using mutt 1.4, and it sometimes gets the threads wrong. The symptom is that some messages of a thread wil appear in an entirely unrelated thread..
My observation is that if someone with mutt-1.2.5 replies to a message by user1, it generates the following header: In-Reply-To: <"from user1"@host1.org> Replies to other messages from user1 in an entirely unrelated thread will also get the same In-Reply-To. my mutt 1.4 seems to conclude that if the Reply-To is identical, then its the same thread. (maybe it even ignores the References: ??) Anyway, I'm not sure who is wrong, maybe both versions?