I found a bug in JBoss 3.0.2 (JDK 1.4.0, Windows 2000) when deploying a JAR-File with a irregular Manifest-File. I wanted to comment out the Class-Path entry with a #. JBoss doesn't do anything. It does not deploy any EJB and outputs no error message.
BTW: I deployed the same JAR-File at JBoss 2.4.4. and it outputs a IOException.
Maybe you can verify the error and fix it.
Bugs should be posted to SF bug tracker (www.sf.net/projects/jboss). I'm not sure we do any manifest handling beyond what is implemented in Sun's URLClassloader, I could be wrong though.