In order to avoid certain Windows restrictions, IE re-implements almost all the controls visible on a web page.
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The Internet Explorer team went and reimplemented all of the controls that a web page would need. They have their own windowless checkbox control, a windowless listbox control,
a windowless edit box, and so on. In addition to reproducing all the functionality of the windowed controls, the Internet Explorer folks also had to reproduce the "look" of the
windowed controls, down to the last pixel. (Functions like
DrawThemeBackground and DrawFrameControl prove extremely helpful here.)
If I recall correctly, the only element that is still windowed is the <SELECT> element.
If you squint, you can see some places where they didn't quite nail it. For example, if you right-click in a text box, options like "Right to left reading order" and "Insert Unicode control character" are missing. As another example, notice that IE's scroll bars do not light up when you hover over them.
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Without seeing the code implementing your page, I would guess that this is another manifestation of "IE's controls don't act native".
If you have a support contract with Microsoft, I'd suggest complaining to them through that channel; if not, see if you get any responses in the microsoft.public.internetexplorer.general newsgroup. Back in IE6, they broke the scrollbar with KB824145 and fixed it with KB832894, so it's not like theses sorts of problems haven't happened and been resolved before.