I've got this problem too. I've searched everywhere I can think of for stray copies of gluegen-rt.jar, but without success -- I've found some copies but the problem is still there. Can you give any hints about where one can look to find these unwanted copies?
Also, I only see this problem with webstarts. I try to activate the vm option "-verbose:class" in the jnlp file by adding
in the <j2se> tag, but I don't see any verbose output on the java console.
Thanks in advance for any tips.