I'm running into this problem rather frequently as well. I've bebuilt all my mailboxes just to be sure, and it's made no difference.
Has anyone figured this one out yet?
It normally happens on my inbox when I'm opening Mail.app (complains about it already being open) and on my deleted items box when shutting down Mail.app.
I've had it happen on a few other of my mailboxes as well, but it's less frequent than the inbox and deleted items boxes.
I've also checked the file perms & ownership to make sure nothing strange was going on there either.