Yes. I guess you have both the SAR and EJB inside the same EAR file. The MBean in the SAR willl be started before the EAR deployment is complete. Until the EAR deployment is complete, the EJB will not be found in the JNDI tree.
One way around this, crusty but works, is to change your mbean to have an internal thread. Have this thread started from the mbean start method. At the start of the thread run method have loop that polls once every second for the EJB name appearing in the JNDI.