Hi Beth,
If it were my site what I would do is since you have identified the file(s) containing css that causes the problem, then do some further troubleshooting to find the specific CSS selectors/rules causing the problem by chopping everything out of the file(s) and then putting them back one by one until the problem re-appears. Once it does see if you really need the rule that is causing it, if not remove it else add something to an ie specific css file to override it.
Hope that helps,
Joe