I don't entirely understand what you mean by 'if you do it without terminal' 
but, if I just run firefox from a launcher, and then click a link in say, 
evolution I get the same effect. 
It appears that firefox ipc isn't working for some reason or the other. firefox 
-new-tab <url> also gives the same results

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firefox fails to open external links when already running
https://bugs.launchpad.net/bugs/125464
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