It has to be environmental. I don't think there would be anything that would affect performance. it's the same thing basically.
Have you checked the place where data is placed? No mounts.. nothing different?
I have JBoss and HornetQ on the same partition on the disc and there are no mounts on that server.
Could there be extra transaction overheads when running in JBoss by default? In both cases I am using the non-XA connections so I don't believe its a quality of service overhead issue.
there will be if your using MDB's, otherwise the only other overheads are the other jboss services.