There may be something wrong in the mimeTypes.rdf file in the Firefox
profile folder, which contains settings for Applications that are opened
for different filetypes and download actions, including mailto actions.
I would try renaming that file to mimeTypes.rdfOLD with Firefox closed
and the restarting Firefox, which will generate a new mimeTypes.rdf
file. You can open the Firefox profile folder from the Help ->
Troubleshooting menu by clicking the Profile Folder button in the
Application Basics section.
You could also try manually selecting Thunderbird as the program to use
for mailto actions in your Firefox Options - Applications panel, even if
Thunderbird is already listed, by opening the drop-down menu for
"mailto", selecting "use other" and then clicking the "Browse" button.
See:
http://kb.mozillazine.org/Changing_the_mail_program_used_in_Firefox#Choosing_a_different_mail_program_to_use_in_Firefox
A third option is to create a new Firefox profile - see
https://support.mozilla.org/kb/profile-manager-create-and-remove-firefox-profiles
(or use the "Reset Firefox" option in the Troubleshooting Information
page, but that may be overkill).