Here's an article I found a while ago that was very helpful in creating CSS drop down menus for IE. From what I understand you have two choices on how to fix them not working in IE. One is using IE hacks to work around some IE issues. The other is using a modified .htc file. This solution uses the hover.htc file to make IE work.
Has a very detailed guide on how to create both verticle and horizontal CSS drop down menus. Hope that's helpful!