I run JEmptool (org.jempeg.empeg.emptool.Main) succesfully on the following config:

Redhat Linux 2.4.2-2
java version "1.3.1"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.3.1-b24)
Java HotSpot(TM) Client VM (build 1.3.1-b24, mixed mode)
Empeg Mk2
One network interface

I haven't compiled the javax.comm libraries for Linux to test serial, but I did ethernet discovery just fine.

If you continue to have problems, I may give you a jar file with some more debug information in it. You can try this:

java -classpath comm.jar:jemplode20.jar:tffid3.jar -Ddebug=true org.jempeg.empeg.emptool.Main

And see what it prints out...

Mike