OK...I know the answer to this now...sort of. For a different thread, I went and checked the stardock newsgroups, and someone there had reported similar problems. Apparently, plugings in IE seem to prevent it from honouring the clipping of the window frame off the screen when maximized.
I've just confirmed this myself as the Google bar I had installed was making IE misbehave, and when I turned that off and re-started IE it works as it should. Apparently Java has the same effect, so visiting a page which uses it (if you have it installed of course) will start IE acting incorrectly too (though I've not verified this myself). The implication is that any IE plugings seem to break WindowBlinds making it crop the window frames off the screen.
Try it and see if it works for you rather than my previous advice. And as an aside, if you currently use the google bar and don't want to be without it, check out their "labs" page and see if the goodle deskbar will work even better...I'm a convert to this new way of using google...