When you set up your server to be bound to IPv6 (but you don't bind the management port to anything), the server fails to stop. Second attempt will force the server to stop.

This is the error in the log:

!ENTRY org.eclipse.wst.server.core 4 0 2012-07-02 16:49:05.284
!MESSAGE Server jboss-eap-6.0.0.GA failed to stop.

This happens most probably because in such scenario, the management port is bound to IPv4 localhost (127.0.0.1).

Indeed I just verified that this is not related to IPv6 specifically but any host name other than localhost - if you don't check "Expose your management port" (and don't set -Dmanagement manually) and the hostname is something else than localhost, then this issue will arise. Note that with remote servers you don't need to bind the management port to anything for server stop to work. So we either need to set -Dmanagement always or make sure it is not needed.