EAP6 restart does not work properly

Issue

• Restart operation fails to start EAP when shutdown hasn't completed and start script is invoked
• When using custom start-script to start EAP 6, JON starts restart but does not finish it. As a result EAP 6 is down but not started again.
• Our EAP 6 custom start script checks if the process is still running and if that is the case, it will not start a new one:

...
       status
       check=$?
       # If already running then do not attempt to start it twice. Also set the
       # value of exit code i.e. RETVAL to 0
       if [ $check -eq 0 ]; then
         echo -n -e " Not starting it Twice \n"
         RETVAL=0
         return $RETVAL
       fi
       ...

However, with this script, when trying to restart EAP 6 instance, our server is shut down but it's not started again (we get "Not starting it Twice" message). What is the problem?