Hi Markus,
In my blog I explained the problem with a logging example. This is just an example, and it does by no means imply that the problem is caused by that. What we do know is that there are references from the application server (or perhaps JVM) to your application. That may be a problem in your application, but it's also possible that there's a bug in GlassFish.
Either way, I think it's worthwhile to dig a little deeper into this problem. I don't think you need to resign to having to restart the server to work around this problem.
I've described some other causes and how to diagnose the problem in detail here:
http://blogs.sun.com/fkieviet/entry/how_to_fix_the_dreaded
Frank
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