A>shutdown.bat -S
A>не помогает?

Помогает, но только если запущена дефолтовая конфигурация.
А если запущена какая-то кастомная конфигурация, например web, то не помогает.

C:\jboss-5.1.0.GA\bin>shutdown.bat -S
Exception in thread "main" javax.naming.CommunicationException: Could not obtain connection to any of these urls: localhost:1099 [Root exception is javax.naming.CommunicationException: Failed to connect to
server localhost/127.0.0.1:1099 [Root exception is javax.naming.ServiceUnavailableException: Failed to connect to server localhost/127.0.0.1:1099 [Root exception is java.net.ConnectException: Connection ref
used: connect]]]
        at org.jnp.interfaces.NamingContext.checkRef(NamingContext.java:1763)
        at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:693)
        at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:686)
        at javax.naming.InitialContext.lookup(InitialContext.java:351)
        at org.jboss.Shutdown.main(Shutdown.java:219)
Caused by: javax.naming.CommunicationException: Failed to connect to server localhost/127.0.0.1:1099 [Root exception is javax.naming.ServiceUnavailableException: Failed to connect to server localhost/127.0.
0.1:1099 [Root exception is java.net.ConnectException: Connection refused: connect]]
        at org.jnp.interfaces.NamingContext.getServer(NamingContext.java:335)
        at org.jnp.interfaces.NamingContext.checkRef(NamingContext.java:1734)
        ... 4 more