I had some similar problems with 3.2.1 - deployment definitly changed in the new release at some points.
The following would be a workaround - not very nice one I have to admit, but should work:
You could package in the following way:
extract all classes (i.e. interfaces and transfer classes) you access from your mbeans from your ear in a new jar - let's call it ear-ifc.jar
Create a sar-archive. There you put in your jboss-service.xml your service jar, your ear (without the ifc classes) and your ear-ifc.jar.
Now you don't get that duplicate class definition. During deployment of that sar-archive the normal jars will be deployed before the ear (since the ear-deployer in 3.2.1 isn't ready at that point), when the ear deployer gets ready the ear-ifc.jar is already deployed so that the ear finds its ifc-classes