Gregor Zattler mentioned some problems with threading at 

       id:20120126004024.GA13704@shi.workgroup

After some off list discussions, I believe I have a smaller test case.

The attached maildir contains 24 messages from the org mode list.

According to notmuch, these form one thread, but I can't figure out
exactly why. It seems like the chronologically first two messages should
be a seperate thread. There are several of the infamous malformed ME-E
In-reply-to headers, but each of these messages also has a References
header; this seems to indicate a case missed by commit cf8aaafbad68.