I previously wrote about how to get the Java-plugin working in Firefox on Ubuntu 8.* on an Intel 32 bit system. After upgrading to Ubuntu 9.04 on an AMD64 system I had the same problem. Instead of a working Java applet I just got a grey box. I had already installed Sun’s Java implementation and tested the previously suggested solution. This was apparently not enough.
The solution was however quite simple. Some users in the Ubuntu forums suggeste removing IcedTea and OpenJDK and so I did. I used the Synaptic package manager but you may also remove it using apt-get: sudo apt-get remove gcj libgcj-common libgcj7-0 icedtea-gcjwebplugin openjdk-6-jdk openjdk-6-jre opendjdk-6-jre-headless libaccess-bridge-java tzdata-java (I have not tested this myself). After removing the open Java implementation you simply restart your browser and that should be it.