If you're using vertical-align or valign then that's the problem since it doesn't work well for divs in IE.
try to go with a table cell, or use absolute positioning:
Code:
<html>
<body leftmargin="0px" topmargin="0px">
Using absolute positioning
<div style="width:300px;height:300px;border:solid 1px #000000;">
<div style="left:100px;top:100px;width:100px;height:100px;border:solid 1px #000000;position:absolute;z-index:2">
</div>
</div>
Using table cells
<table cellspacing="0px">
<tr>
<td align="center" valign="middle" width="300px" height="300px" style="border:solid 1px #000000">
<div style="width:100px;height:100px;border:solid 1px #000000;"></div>
</td>
</tr>
</table>
</body>
</html>