I can't say whether it's exactly the same problem you're seeing but I couldn't get Vosao (cookie based)'s authentication work with cloud endpoints.
The reason is that the way endpoints is implemented (in Java, at least), there's a servlet listening to Rest requests that internally posts RPC request to another servlet.
This mechanism means that the cookie from the first request is passed on to the second request, but for subsequent requests the internal "socket" between the two servlet was already established with the first request. Therefore all subsequent requests are authenticated as if they were coming from the first user, a security nightmare.
There might be away around it, for example avoiding Rest requests altogether and using RPC directly