Here is the root cause:
>>Caused by: java.lang.ClassNotFoundException: org.jnp.interfaces.NamingContextFactory
That class appears in several JAR file but I suspect that shutdown will use the one from client/jnp-client.jar (or perhaps client/jbossjmx-ant.jar) based on the classpath set on line 67 of shutdown.sh.
I suspect that there is something wrong in your setup. I would look at the following:
1) Did you make any changes to shutdown.sh?
2) Verify that the two JAR files I mentioned exist.
3) Do you have JBOSS_HOME set? If so, unset it! The shutdown script will set it automatically.
4) Determine the full command line passed to the java process (for shutdown). You can do this by either running ps while the java process is running (could be tricky, it won't run long), or by editing the shutdown.sh to echo the command.