Did you check if there are error messages reported in the server.log?
When stopping the server in JBoss Developer studio, the error message is displayed, but nothing actually happens. The server is not stopped. There is nothing written to the log files. Clicking the stop button a second time actually performs the stop correctly.
Apparently this issue occurred already some time ago. But I am not sure whether this had been solved yet (JBoss EAP 6 requires two stop commands to really stop )
It looks like this could also be caused by some conflict with other AS instances.
Do you also have similar issues with other servers?