I have the same problem. I am just evaluating JBoss 7.02 and I just created a super simple program with one normal pojo containing a reference to a stateless EJB using CDI. It works ok but when I change one of the files it looks like it is publishing but nothing happens. When I use "Clear" on the server instance it works ok again.
Publishing settings on server: "Automatically publish when resources change".
My stuff: JBoss 7.02, Eclipse 3.7 indigo with latests JBoss Tools from update site http://download.jboss.org/jbosstools/updates/development/indigo/