I think I've found a reason to this problem, the package making the libjavaplugin.so symlinks (whichever it is) is creating the symlink in /usr/lib/mozilla-firefox/plugins/ this was no problem on Feisty since /usr/lib/mozilla-firefox was a symlink to /usr/lib/firefox. In Gutsy the symlink has been removed, but libjavaplugin.so continues to install the symlink in /usr/lib/mozilla-firefox/plugins where firefox does not look for it anymore.
I think I've found a reason to this problem, the package making the libjavaplugin.so symlinks (whichever it is) is creating the symlink in /usr/lib/ mozilla- firefox/ plugins/ this was no problem on Feisty since /usr/lib/ mozilla- firefox was a symlink to /usr/lib/firefox. In Gutsy the symlink has been removed, but libjavaplugin.so continues to install the symlink in /usr/lib/ mozilla- firefox/ plugins where firefox does not look for it anymore.