We are trying to upgrade to 3.1. Our application is packaged and deployed as an EAR file with multiple EJB and WARs embedded. Some of the WAR files have web services for deployment, and some do not. The 3.1 deployment mechanism is fundamentally broken in this case. It appears that the web service deployment piece ends up scanning all the wars in the EAR for metadata (annotations), and then trying to deploy the collected web services in every WAR in the EAR, not just the one that had the annotated web service classes.
This appears to be the same symptoms as the following bug, but for web services instead.
I have attached a very simple test EAR file. Trying to deploy this will demonstrate the error. You will see error messages about duplicate web service deployments and class not found exceptions.