We are using a database dump and a alf_data copy made from the running site (while tomcat is stopped of course), so I doubt there is a mismatch in code an Database, but we will repeat the process just in case.
We are installing on Debian Squeeze's Tomcat6 package, not vanilla. But the shared class loader is running fine as we have some custom beans defined there as well as the database configuration and they are being correctly loaded (we have some logging on bean initialization), besides I can see the SQL sentences executing against the configured database (which has not the default password nor the default name).