AFAIK when deploying we are calling server via JMX. What happens when JMX call is not successful? Nothing good. Studio shows project as deployed, but app server in worse case does not know about deployment (when target dir is set to workspace), in better case notices it after a few seconds.
User than can only guess what and why is his project not deployed.
This confusing behavior can be simply reproduced on any soa-p server, since you have to uncomment 'admin=admin' line in file /server/default/conf/soa-users.properties to make JMX working. If you do not do that, you'll reproduce.
AS Adapter should warn user on JMX call errors.