Try to copy files in your folder with a temporary extension (es. .lck) and then rename them.
However, it didn't make any difference. Also tried a test where I copied the files first (and let them finish) and then started JBoss. I still see some duplicate messages (same file got picked up twice).
I forgot to mention that we have 2 instances of the app (in 2 Jboss nodes in a cluster) with each having the gateway that is monitoring the same directory. Also, with one JBoss node, I never see the problem.
JBoss SOA-P 4.3 did not have this problem.