Can you check if the wsdl of the published endpoint on AS 6 differs from the one of the same service on AS 5 ?
JBoss AS 5 and 6 come with different default WS stack (6 having JBossWS-CXF), so you might see minor changes in the published wsdl when doing code-first development. While it would be interesting to understand if this is a bug in the way the imported schema is handled in the wsdl, or if it's a consequence of how the namespaces are defined in the jaxb annotated classes, please keep in mind that you can develop starting from a given wsdl you want your services to have (wsconsume tool on the wsdl, then implement the generated service endpoint interface).
Regarding the libs to be used, take a look at the wsrunclient scripts in AS 6 bin folder to have an idea of everything you might need. In your java.endorsed.dirs env variable you should include only the libs that are in lib/endorsed on the AS version you're using. That influences the JAXB/JAXWS api version used when running with JDK6.