Jonathan,
Have you figured out what this bug is? I’ve got the same one and I thought my client was crazy (which is still debatable) since I don’t see it on my IE, but checking on a friend’s computer that has a slightly different IE version pulls up this bug.
If you’re at the top of the page and you click a shadowbox link, it’ll open centered, but if you’re even slightly down the page it’ll open halfway down (darkened background starts halfway down page too). Scrolling down will shoot the shadowbox down the page and out of sight. A shadowbox link that is buried down a long page will pop up out of sight.
Somewhere the math for keeping this centered is getting wonky, but only in certain versions of IE. Can anyone figure this out?