I think you can adjust the nylon "bump stops" that are attached to the window. You'll have to get the door panel off and roll the window down some to get to them. They look like hollow rollers, but their only purpose is to limit the window's travel at the top (that's my theory, at least). Loosen those (I think there are 2) and see if that allows you to roll your window up any further, then tighten them back down.
Of course, there may be a top adjustment I don't know about. I know mine sometimes leaks through where the window gasket splits to allow the top to fold back. I can slide those pieces back together and stop the leak till the next time I cycle the top down and up again.
Hope that helps...