I've often come across similar problems when working with these two browsers, and occasionally the only thing left to do is slightly change it for one of the browsers.
Your post didn't say whether you use seperate stylesheets for each browser? If not then it is a must. It is a small piece of JavaScript that anyone will be able to tell you.
However if you do already use seperate stylesheets, then I can only suggest slightly changing the IE stylesheet. The two browsers simply don't display everything the same.
Hope tht helped
PS - If you need that JavaScript then just ask 
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