Well, IE 6 has enough quirks and bugs that I think it could be possible some combination of css leads to this issue. It may be difficult to figure out what in the css is causing it though. One strategy would be to backup your skin and then start chopping things out of the css and see if you get to a point where the problem does not happen, than gradually put stuff back and figure out what specific css is causing it.
Hope it helps,
Joe