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[peter green <plugwash@xxxxxxxxxxx>]

I have tried and failed to reproduce this in pbuilder, all the java 
plugin packages in debian that i'm aware of ( icedtea-gcjwebplugin, 
icedtea6-plugin, sun-java5-plugin and sun-java6-plugin) seem to handle 
the plugin alternatives in the same way which seems pretty sane to me 
and unless multiple plugin dirs are symlinked together or something else 
is messing with the alteratives I can't see how this could happen on 
upgrade from -3 to -4.

Have you ever installed a java plugin package from a non-debian source?
Is either /usr/lib/mozilla/plugins or /usr/lib/iceweasel/plugins a 
symlink on your system? If it is where does it point and do you have any 
idea how it got that way?
What does /etc/alternatives/iceweasel-javaplugin.so point to?