I think the best way to run the client is to choose Webstart OR the standalone package. Mixing things is a recipe for problems like yours
The standalone package is imho best for people that want to run a node 24/7 or only want to run NIS. Webstart is meant for people that just want to use the client and have an easy way of starting it.
Nobody is mixing anything though.
I understand that things are setup this way to accommodate those that go for the One Click Install but it causes this issue when running everything through the Standalone Package. Not saying that the issue is critical (or even important for the matter)... we just need to point to the solution when people report having this particular problem.
Indeed that seems to be something we haven't thought of. We'll find a solution for that.