I'm not totally understanding the setup that's leading to the problem, but you might want to explore the useIFrame property of the YUI Autocomplete object -- it layers an iframe object beneath the autocomplete field, which allows the field to then float above the objects that are obscuring it in IE's buggy layout.
http://developer.yahoo.com/yui/docs/YAHOO.widget.AutoComplete.html#property_useIFrame
But the docs say that this matters in 5.5 < IE < 7, so this might not be the issue you're experiencing. So again, without totally understanding the setup you're working with, you might also want to try to experiment with various z-index values for the autocomplete field and the surrounding block-level elements.