Attempted to deploy an EAR containing a RAR and an EJB JAR with an MDB in to Geronimo M3. Got a stack trace including a message that my openejb-jar.xml syntax was wrong (was still using pre-M3 openejb-jar.xml). Updated syntax, rebuilt, and tried to deploy again. Got the same message again referencing the old DD content. Double-checked that application was updated; it was. Tried again, same message. Stopped and started server and tried the deploy again, and it worked. It seems like repeated deploy attempts while the server is running just attempt to deploy the original code again instead of seeing the new code.
I have not tried this on HEAD.