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[Kimmo Storbacka <kimmo.storbacka@xxxxxxxxxxxxx>]

After running the latest updates it seems to have solved some of the
problems. I can use some Java applications now, but not all...

Sometimes it still leaves one of the CPU cores running on 100% when
loading some Java app fails, even after closing Firefox. Have to kill
the java-process manually.

-- 
icedtea6-plugin not compatible with Firefox 3.6+
https://bugs.launchpad.net/bugs/496097
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which is subscribed to openjdk-6 in ubuntu.

Status in “openjdk-6” package in Ubuntu: Triaged

Bug description:
Starting in Firefox 3.6, Mozilla foundation will drop support for OJI (Open Java Virtual Machine Integration) that icedtea6-plugin uses, and will only support the standard NPAPI and NPRuntime interfaces.

This is already working in openjdk mercurial as described here:

http://dbhole.wordpress.com/2009/08/26/icedtea-java-plugin-with-chromium-and-firefox-3-6a1/