I think I am seeing a similar bug, and I may have a workaround. The CPU%
goes up to 51.1 shortly after starting Firefox and stays there,
regardless of number of open windows/tabs, Flash, no Flash, etc. sites.

After a while, the Firefox windows eventually fade to dark, as if
"thinking," but never come back and I have to kill.

I'm in Ubuntu Intrepid 2.6.27-16-generic, Firefox version info:
Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1.2) Gecko/20090729
Firefox/3.5.2

Searching online, I found the suggestion that there was a problem with
the default Firefox theme in Ubuntu. Sounded weird, but I don't develop
this stuff, so I downloaded some new 3.5 themes. After installing *any*
of them, my CPU% has gone down to 16% or lower, and does seem to change
depending on number of tabs open, complexity of pages, etc.

You might want to try this. I'm currently using a theme called
"Charamel" with no problems so far (1 day).

-- 
Firefox use a lot of processor doing nothing
https://bugs.launchpad.net/bugs/449664
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