While not an option for a shipped profile, changing these lines:
  /usr/lib/jvm/java-6-openjdk/jre/bin/java Uxr,
  /usr/lib/jvm/java-*-sun-1.*/jre/bin/java Uxr,

to:
  /usr/lib/jvm/java-6-openjdk/jre/bin/java uxr,
  /usr/lib/jvm/java-*-sun-1.*/jre/bin/java uxr,

worked. Apparently too much is being scrubbed from the environment.

** Changed in: linux (Ubuntu)
       Status: Incomplete => Triaged

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

-- 
apparmor profile freezes Firefox when using Java
https://bugs.launchpad.net/bugs/484148
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