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Problem:

IE, in all it’s versions, ignores the z-index from non child elements, meaning that if you have a div inside another with z-index it’s fine, however, if there’s an external div (99%) of the cases, it will simply ignore the z-index.

Solution:

There’s no solution for this, but you can do a workaround. Even with IE ignoring the z-indexes it does has an order of placing elements in front of the others which is the order you have them on html, so if you have a header menu that should appear in the top of everything, you can place the html in the footer of the page, with position absolute, to the header position. This might not work for all cases, but helped mine. since the div in question was hidden and would appear when a element at header was clicked.