Ok, some further information.
If I start the server after removing my app from the deploy directory behaviour is exactly the same.
Guess I'm migrating to CR2.
How much changed in this release? It couldn't have been that much I hope.
Can I just copy libraries into a CR1 release on JbossAS5?
For anyone who's interested the only things that changed in CR2 regarding a JBoss5 install are the libs and the hornetq-ra.rar folder in the deploy directory.
So if your upgrading from CR1 you can save yourself some time by copying these from a fresh JBoss build into your CR1 JBoss build removing the need to reconfigure the whole of JBoss again.