I found a link last night which may be relevant, but for some reason was locked out of this thread. The computer rebooted overnight and now I can't find the article again, but the gist of it was that a corrupt prefs_js file could cause this.
Unihide your files, browse to your Firefox profile and rename that file or any backup copies of it. You DON'T want the auto backups to load in its place as they will also be corrupt
When you reboot the machine and fire up Thunderbird a new preferences file should be created (though without any personal tweaks)