I've noticed this also.
My solution was to not use shutdown, just check is the bootstrap was started or not and to deploy/undeploy my EJB3, JMS queues and topics, ...
It works fine for EJBs. Unfortunately for JMS queues and topics, if I undeploy the topics, when I try to redeploy it, topics is not deployed.
As I use Embedded for JUnit tests that's a big issues.
So redeployment of queues/topics doesn't work? That should work, i'll create a unit test.
Currently though, you cannot boostrap more than once. Look at the unit test samples and how they work.