After some experimenting, I finally found the problem. I knew of the MANIFEST.MF problem regarding the newline at the end of Class-Path entries. Since the mentioned SilverStream application server does not use the JDK classloaders but its own implementation, this "bug" did not occur.
Adding a newline at the end of each Class-Path entry throughout the ear solved the problem.
I still have the log4j problem however.
Can it be turned off in 3.0 ?