Thanks for the answer Maneesh!
I found that when running firefox as root in Ubuntu Linux, the jar files were recognized as signed and the application ran without problem. I checked the suggestion of that post, but my computer did already have "keep temporary internet files" checked in the java control panel, so for me that was not the problem. For a user to have to be running the web browser as root to recognize the jar files as signed does not seem optimal, but its good enough for me for now.
I will wait with marking this thread as solved, since it still seems a bit mysterious to me that a linux user would need to launch for example firefox with "sudo firefox" in order to view webstart applications...
i wrote a blogpost about my adventure with webstart, it is a little unspecific, but it has some more details about what worked and didn't work for me if anyone has similar problems: http://www.beardtowncoop.dinstudio.com/
subject: signed jar-file gives error "Found unsigned entry in Resource"