Can you please attach your kern.log after getting the permission denied?
Also, what version of zotero are you using?
** Also affects: firefox-3.5 (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: firefox-3.5 (Ubuntu)
       Status: New => Triaged

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[karmic] evince apparmor profile breaks zotero reference database
https://bugs.launchpad.net/bugs/449286
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