Comment 1 for bug 600642

sun-java5-plugin is not supported by FF3.6 (that was mentioned in the release notes section of the USN, and is also mentioned in the firefox changelog)

sun-java6-plugin should be working fine, but you might have another java plugin on your system that the alternatives system is pointing to instead.

Could you please post the output "update-alternatives --display mozilla-javaplugin.so"? (Also, feel free to post the same output for xulrunner-javaplugin.so and firefox-javaplugin.so)