This is my first bugreport... if I'm doing something wrong or chose the wrong component (something) - please be forgiving
so I had a couple days to figure this one out - the deployment assembly is misbehaving similarly (but differnt) to older versions when it was used under a different name (J2EE module dependencies i think).
So when I add a folder e.g. WebContent and want it to deploy to / it will not work or more accurately - under certain circumstances it will stop working. E.g. I think after adding some additional libraries to deploy to webcontent/lib. I suspect the problem is that it gets deleted before deploying. The workaround for me was to use a fileset of the <projectname>/WebContent folder and to point it to an empty deploy path - and to scream in rage at everyone who dared to touch any settings in there.