I've been using enigmail inside Thunderbird for mail for a while now. However, the default setting was such that mutt wasn't auto-detecting the messages as encrypted when I was sending them, because the content-type wasn't set – programs had to look for the “BEGIN PGP MESSAGE” line.
It took a bit of hunting, but I was finally able to figure out how to change this. Since it's non-obvious, here's what you need to do:
You can't change this option from the main “Preferences” window for Enigmail, you have to do it from the Composition window. That's what tripped me up.