I've never had any problem with IE6 and height: values, but a quick Google search led me to this [zeldman.com] Jeffrey Zeldman page, and an interesting section on the "IE/Win float flub".
IE6/Win has a problem calculating the height of CSS layout elements that float left or right. Once it has calculated a height value for a floated object, IE caches it instead of recalculating as the visitor travels from page to page.
The solution they propose is to refresh the page, forcing IE6 to recalculate the height values.
I'm not sure if this is what you are encountering, if it's not where are you seeing this in action?