I fixed this problem by doing the following:

Open "mailto" links in thunderbird

open firefox
select edit preferences
select applications
locate "mailto"
modify "mailto" to point to: /usr/bin/thunderbird


Thunderbird links won't open in Firefox

open thunderbird
edit, preferences, advanced, config editor
right click, new, string
string name: network.protocol-handler.app.ftp
string value: /usr/bin/firefox

open thunderbird
edit, preferences, advanced, config editor
right click, new, string
string name: network.protocol-handler.app.http
string value: /usr/bin/firefox

open thunderbird
edit, preferences, advanced, config editor
right click, new, string
string name: network.protocol-handler.app.https
string value: /usr/bin/firefox

restart thunderbird

-- 
mailto links in Firefox 3.0b5 do not open up Thunderbird compose windows
https://bugs.launchpad.net/bugs/222944
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