Hmm.. I think most of the problem is that Java executes pretty slowly in comparison to many other languages. This happens on my girlfriends computer too (to a lesser extent). It's a really weird problem since it seems that only better computers run into it. Do you have a 64 bit processor?
She just kinda got used to it. I hate to tell you to do that, but it's really the best answer I have for you right now. I was contemplating making an alternate version in C# in the future. That's if I get bored, of course. Until then, sorry =(