I do see what you mean. I’ve noticed that the animation’s a little stilted in some browsers too, although it seems particularly bad on your site. It may have something to do with the fact that there’s quite a lot of javascript running on your page. Then again, nothing else is really being called at the exact same moment as Wikipop, so it’s hard to say if that’s actually the issue.
In any case, the problem results from the fact that Wikipop performs the animation at the same time that it’s loading the Wikipedia page into the frame. I experimented briefly with loading the page content when you rolled your cursor over a link, so it would already be loaded when you actually clicked the link. It did sort of work, but it would also be terrible practice from a UI perspective.
