A: 

Make sure the JNLP file is not cached. I.e., each time you try something new, have you renamed / relocated the JNLP file?


Regarding your updates,
The only ting that comes to my mind is that you need to make sure that your script responds with the correct mime type: application/x-java-jnlp-file

That is, from your cgi-script, you have to provide the HTTP header field

Content-Type: application/x-java-jnlp-file
aioobe
renaming is slightly problematic as the JNLP files are generated by a script, but I have tried to run the application on new computers (read: never been exposed to the application) and even restarted my browser/machine a couple of times. That should effectively empty the cache right?
posdef
Hmm.. yeah. Then it's really strange. You should do a minimal test-case that fails and post your specific OS / Java-version and example
aioobe
yeah, the question is what constitutes a minimal-case scenario?
posdef
That's only possible for you to narrow down on.
aioobe
hmm, i guess...
posdef