I had the same problem and it was the div that was surrounding most of the stuff in the line1 div in head.tpl. I had to add a z-index that was the same as minicart-box to the div that surrounded everything.
ex:
<div id="quick-cart"> <------------this div is absolutely positioned but had no z-index so i added one
.....blah blah stuff....cart stuff included....
</div>
Hope this helps
Oh and I'm on xcart 4.3.2