I'm getting the exact same error, what was the resolution then?
Besides, when you say ./jboss-cli.sh -c --file=deploy.scr does work, do you have to copy the components separately into the server?
I'm getting
Path /home/me/JAVA/jboss-as-7.2.0.Alpha1-SNAPSHOT/bin/jtds-1.2.6.jar doesn't exist.