I got similar behaviour. Same system & java version.
When I open an applet it is shown correct. Then after reloading or opening a
new applet/java-window it is most times grey (sometimes its shown normal).
The problem can be solved the same way like the compitz-swing-problem:
export AWT_TOOLKIT="MToolkit"
But I don't like this workaround, because it just looks ugly and is
buggy.
Java 5 is working correct in Firefox. And in Epiphany even java 6 works.
So I'm using Epiphany for all java applets...
** Changed in: firefox-3.0 (Ubuntu)
Status: New => Confirmed
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Java applets are working only one time from launching Mozilla Firefox 3 b5...
https://bugs.launchpad.net/bugs/223764
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