I have experienced the same message popping up while eclipse (europa) and 
firefox (2.0.0.11) running on gutsy gibbon.
The message popped up 2-3 times during the day.

I have created the above directory and have not had the problem since...

I noticed there is a new file in this directory (prefs.js) - see
attached.



** Attachment added: "prefs.js"
   http://launchpadlibrarian.net/11788919/prefs.js

-- 
[Hardy] Eclipse applications show error "Could not initialize the application's 
security component" 
https://bugs.launchpad.net/bugs/188380
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