For those of you using GPGMail to sign or encrypt your mail, you might want to check which version you are using. An update (GPGMail 1.0.1 (v33)) sneaked past me late last year and it has some important fixes, like no longer leaving orphan GPGMEProxyServer processes on a quit or a crash. I can't prove it, but I think this issue was causing me a lot of problems with Mail.app and since the update, all has been clear.

Then again, it could have been those darn flying elves...