Are you in KDE? gnome? xfce?
Please check what the settings are in System>preference>preferred.....
This happens more so ok KDE than the others. This is due to lack of QT support 
at this time. Can you please give me more info about your system? some examples 
follow, These are not the only ones we need so any other info would be great:
lsb_release -a
apt-cache policy firefox
apt-cache policy firefox-3.5
apt-cache policy firefox-3.6
apt-cache policy thunderbird
apt-cache policy thunderbird-3.0
Any other info would be great :)

** Changed in: mozilla-thunderbird (Ubuntu)
   Importance: Undecided => Low

** Changed in: mozilla-thunderbird (Ubuntu)
       Status: New => Incomplete

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Thunderbird hyperlinks don't launch browser
https://bugs.launchpad.net/bugs/363577
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