Comment 5 for bug 1427144

I also had this problem, not only with links in Thunderbird but also in Libreoffice documents, which both opened Firefox at my chosen homepage, not the link URL.
I have always changed my Preferred Application setting in XFCE Settings-manager to firefox rather than Debian Sensible Browser which is the default, and this never before caused any problem. With the upgrade to FF36 this seems to have broken.
Changing the Preferred Application back to Debian Sensible Browser seems to have fixed this and links are again opening in Firefox to the URL of the clicked link.
I have not tested George Shuklin's solution above yet, but will investigate later.

I have responded to a Ubuntuforum post with this and previous workarounds for this problem
See http://ubuntuforums.org/showthread.php?t=2267439

I am using Xubuntu 14.04.2 64bit.
uname -a output:-
Linux XubuntuTrusty 3.13.0-46-generic #76-Ubuntu SMP Thu Feb 26 18:52:13 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux