I am working ('mean I try !) with eclipse 3.0.1 and JBoss 4.0.0 ; I added a file jboss400.server within the Lomboz plugin directory "com.objectlearn.jdt.j2ee_3.0.1\servers" as recommended in one of the numerous discussions dealing with this frequent issue in JavaRanch: I downloaded the source file from a recommended Japanese Site ;
Finally I could create my J2EE project but now I can't run debug the apps : JBoss Server does not run ! The eclipse console remains blank, and the perspective does not switch to the debug view !
Actually, as far as I can remember I did not change anythingelse ; nevertheless, I advise you to set a "clean" install of Eclipse+Lomboz+JBoss configuration before running eclipse for the first time !
With Eclipse 3.0.1 I experienced that to make it run with a new plugin I had to re-install Eclipse and all the other plugins along before running this "new" Eclipse.
Then, you can try to re-install eclipse and then before running eclipse re-install Lomboz Plugin, copy the file jboss400.server (and this is tricky in fact ; do you find it back in the Lomboz "Preference" configuration ? on my side I had to change an existing one ...) in the proper plugin directory, re-install JBoss 4.0.0 (the previous deployments of your J2EE projects might cause troubles when starting the server ...) ; this worked for me, but I did this 3 or 4 times in a single day !