I have the same effect on upgrade to Jaunty. I don't know which package
is broken, but it looks like the Preferred Applications menu is not
properly updating /etc/alternatives. Though I set firefox to browse web
pages Preferred Applications, /etc/alternatives points to epiphany.

Workaround:

sudo update-alternatives --config x-www-browser
[pick firefox]

but this isn't a fix; this is just a workaround; the auto setting gets
it wrong.

I can't tell what package this belongs to, either, but I suspect it's
whoever owns the System|Preferences|Preferred Applications dialog.

** Changed in: ubuntu
       Status: New => Confirmed

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x-www-browser is launching epiphany even if I have firefox selected as my 
preferred web browser
https://bugs.launchpad.net/bugs/367827
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