I read somewhere that it is not possible to enable the GPS programmatically, but I searched some apps around the market and apparently, Lookout can do this:
I've already said that the problem is probably how your project is structured! Why do you assume that is has anything at all to do with how you export the jar?
The problem is not how you export it, which seems correct, but how your Eclipse project is structured. Please read post #6 in the thread that I linked to in my last reply.