I had the strangest issue with Thunderbird during the last big upgrade, where it took my PGP key out of gpg (deleting the key from the store in the process), and stored it in Thunderbird with no protection. I must have read an encrypted email for it to have used the password, but I have no idea how this happened, and do not click "Yes" on boxes without reading them thoroughly. It took me a month of my PGP key apparently sitting unprotected before I noticed.

The fact that Thunderbird does stuff like this to me really weirds me out, despite mostly loving the program.