By default JBoss AS Adapter uses .metadata/.plugins/org.jboss.ide.eclipse.as.core/JBoss-AS-5.1.0.GA/deploy folder to deploy your project and then registed this temp folder in JBoss AS throug JMX. It might not working properly for JBoss 6.0.0. I would try direct publishing to server deploy folder:
1. Open Srver configuration by double click on your server instance in Servers view
2. Go to Deployment tab and select "Use the JBoss Deploy folder"
3. Save Server configuration
4. Select your project on server and make a "Ful Publish" using project context menu
5. Start server
I hope it helps.