The java.lang.RuntimeException: Failed to initialize prefs api. java.lang.InternalError: Can't instantiate Preferences factory java.lang.ClassNotFoundException: org.apache.jetspeed.prefs.impl.PreferencesFactoryImpl is caused by a bug in earlier versions of JDK 1.4 documented here: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5012893.
Basically, you will need to be on JDK JDK1.4.2_04 or greater.
This can also be related to not having the correct dataSource jndi name defined.