Comment 17 for bug 288397

It seems that "auto" has been disabled on the symlinks if the update-java-alternatives has been used.

So to for the update-alternatives to work, auto first has to be set on the plugins:

update-alternatives --auto xulrunner-1.9-javaplugin.so
update-alternatives --auto xulrunner-javaplugin.so
update-alternatives --auto firefox-javaplugin.so
update-alternatives --auto mozilla-javaplugin.so

sudo update-alternatives --install /usr/lib/xulrunner-1.9.0.4/plugins/libjavaplugin.so xulrunner-1.9-javaplugin.so /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so 100
sudo update-alternatives --install /usr/lib/xulrunner/libjavaplugin.so xulrunner-javaplugin.so /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so 100
sudo update-alternatives --install /usr/lib/firefox/plugins/libjavaplugin.so firefox-javaplugin.so /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so 100
sudo update-alternatives --install /usr/lib/mozilla/plugins/libjavaplugin.so mozilla-javaplugin.so /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so 100

But all this should really be done in the deb, why still ship a broken plugin when there is a working alternative?