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?

-- 
The old plugin hangs firefox 3 when loading java applets
https://bugs.launchpad.net/bugs/288397
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