I need to use friefox 3.6 for applications here at work (Domino Web Access - iNotes) So even though I had everything defined correctly, the "Send Link.." wasn't working to send email via thunderbird. I realised in the stderr on firefox it would say:
/usr/lib/thunderbird/thunderbird-bin: /opt/firefox/libnss3.so: version `NSS_3.12.10' not found (required by /usr/lib/thunderbird/libxul.so)
So I guessed that this had something to do with the fact that I was still running a stock Firefox 3 and library incompatibilities with the newer thunderbird. Instead of downgrading tbird, I decided to edit the /usr/bin/thunderbird startup script. I first debugged it buy putting an "env|sort" right before it kicked off the app at the bottom. Found all references to /opt/firefox and overrode them, pointing to /usr/lib/thunderbird instead.
Put that in a file called /usr/bin/thunderbird-firefox and made that the default email client.