I had the same trouble when i upgrade from Gutsy to Hardy, i was using FF3 beta 
4 and Thunderbird 2. Now i found a solution:
1.- Close both apps.
2.- Locate the ~/.mozilla-thunderbird/xxxxxx.profile/ directory, where xxxxxx 
are a chain of numbers and characters.
3.- Find the file prefs.js open and add the next three lines:

user_pref("network.protocol-handler.app.http", "/usr/bin/firefox");
user_pref("network.protocol-handler.app.https", "/usr/bin/firefox");
user_pref("network.protocol-handler.app.ftp", "/usr/bin/firefox");

4.- Save, close and test.

I founded here: http://www.forosdelweb.com/f41/como-howto-integrar-
mozilla-thunderbird-con-mozilla-firefox-312158/

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