I take it back .. That's too annoying. Go get
http://www.jempeg.org/debug.zip
unzip jemplode20.jar, unzip debug.zip on top of it (it should replace about 6 or 7 files) then zip jemplode20.jar back up again. Alternatively you can unzip debug.zip and then zip -ru jemplode20.jar to update it and replace the files. Then run jemplode again and send me the console output. If you don't get console output, open jEmplode 2.0.lax and search for "stdout" and you should see a line that defines where stdout redirects to .. set that equal to "console" or a filename and then rerun.
What this does is print out the name of each soup, the total number of tunes in the soup vs. the total number of tunes on your Empeg and if there are any in the db that aren't in the soup, it prints out which ones. For a soup that doesn't have any searches in it, the total number of tunes in the soup should always equal the total number of tunes on your Empeg. If you have a search anywhere in the chain, the search can filter out some, so it's ok to have missing tunes in that case.
You may want to keep a copy of the original jemplode20.jar, since this debugging slows down soups a lot.
I think I did everything right I set stdout to redirect to a file but I don't get anything and I am not sure what you mean by console. What should I be watching.
Thanks
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Matt