This may sound crazy, and i didnt believe it until i saw it for myself.
The vertical scroll bar does not scroll when you click in the space between the scroller or the arrows. You have to drag the bar to get it to scroll. This only happens in the ugly default theme (not windows classic).
The scroll bar has some heavy javascript behind it that drive scrolling of another DIV on the page.
Has anyone even encountered this before? Why the heck does the theme influence IE's rendering?! Only IE!
edit: this problem happens when you are in "non-classic" XP theme (the default ugly one). switching themes does not cause this, but it does fix it if you switch to classic from the default.
Does it help when you add
<!--[if IE]><meta http-equiv="MSThemeCompatible" content="no"><![endif]-->
to your page source? It worked well to work around glitches in IE when a non-classic theme is enabled for me. Note that the conditional comments are there so that firefox does not parse the tag (because it will screw up scrollbars in firefox sometimes).