It is very hard to say without seeing the live page, so that all markup and styles can be considered together as to their net effect on the presentation in the various browsers. Without that I can only suggest one thing that often works. That is to use absolute positioning:
HTML Code:
<div id="menu" style="height:40px;position:absolute;">
<iframe marginwidth="0" marginheight="0" src="menu.html" frameborder="0" width="100%" scrolling="no"></iframe>
</div>
But, this can throw it off in the other direction, causing overlaps so, then a container with relative positioning:
HTML Code:
<div style="height:40px;position:relative;">
<div id="menu" style="height:40px;position:absolute;">
<iframe marginwidth="0" marginheight="0" src="menu.html" frameborder="0" width="100%" scrolling="no"></iframe>
</div></div>
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