I think that's normal. You see webstart installs NIS on your computer while the standalone package is merely lying around in some location unknown to it.
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.