I'm not sure how to properly submit a bug report but I've noticed this about mixed messages in the Mail threads...
If you view the Raw message (View->Message-Raw Source)
in the "References:" section there are a series of identifiers looking something like...
<0FA100E1002C504EA922B8279AE2998D0133654BB1@someAddress.com>
<E2274F86-B383-4459-B71D-E2B380B85C97@anotherAddress.com>
with only the mail messages that are mixed together there are unusual identifiers that look like...
<,<0FA100E1002C504EA922B8279AE2998D0133654D32@someAddress.com> <>>
notice the extra "<," and trailing "<>>"
on threads that work correctly I do not notice this. I'm not sure if this is indeed the problem or of anyway to fix it, but perhaps this may get seen by someone with more insight and can bump us along to a fix.