I had a similar problem.
Thunderbird (3) has options to set the application to use to open links.  I had 
this set to the correct Firefox installed when I upgraded from 9.10 to 10.04.  
It did not work: links (http or https) would not open.
IMO the bug is that there is more than one place to set the functionality for 
opening links: in this case, one place is in TB, and the other is via 
System>Settings>Preferred Applications.
In my case, at some distant time in the past I had set the Web Browser (and 
mail, too) to open a Custom path
(to an older firefox which I wouldn't expect to work under 10.04).
I think the correct solution would require a Gnome variant of TB to strip the 
ignored and deceptive configuration choice from TB, to be installed as the 
Ubuntu version.  Either that, or only use the system preference as a fallback 
to application-specific preferences.

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https://bugs.launchpad.net/bugs/663100

Title:
  Thunderbird starts Konqueror instead of Firefox when clicking to links
  in mails

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