Player inside out after weight painting

Ok, I know this might be hard to understand but maybe someone has had this problem before and can help me out. Whats wrong is that I have a player mesh rigged with a simple skeleton. The model exported fine with the skeleton until I did the weight painting and made the root animation. It now looks like the leg bones were pulled way up and the arm bones were pulled way down, turning the mesh inside out.(hopefully you understood that) At first it seemed like a bone structure or weight painting problem, but I couldn't find anything wrong. After about an hour of no success I decided to redo the whole skeleton.(I actually did it twice, because I didn't want to have to post this and look like such a noob!) Of course nothing has changed at all. If any of you have any idea of what to do, I would really appreciate a post. Thank you.