As has been pointed out naitve code with Web start is generally not a problem. But I came a cross one HUGE issue with it that prevented me from using it for a project.
I needed to install some native code.. libraries that depended on other libraries that I was distributing.. Some were media codecs from 3rd parties... I tried to use the mechanisms in webstart to install extensions and add paths to runtime so it could find libraries.. and that API did not work. It seems if you have that kind of extension you MUST install stuff in a place that is already in the path because the webstart API is broken. (this was on Windows)
Also there seems to be no way to change the ccurrent directory in Java.. even from native code.. so I had no way of getting libraries into my path.
(I know of tricks to load libraries if you use A and A needs B, just loadLibrary B first and then load A.. but that hack wouldn't work in my situation. )
Btw, this has nothing to do with timers, sorry