From #JbossTools on IRC:

[11:07] <bruth> Another issue: apparently when I change from the default of deploying to .metadata to using the JBoss deploy/ folder, two things don't happen, (1) the files aren't cleaned out from .metadata and (2) the references that tell the JBoss instance to deploy things in the .metadata folder aren't removed, so JBoss starts, deploys from deploy/ then also tries to deploy from .metadata, generating all sorts of duplicate MBean errors