yes, it's true, but you can use a condition like this to deal with compatibility issues:
<? if (isset($_SERVER['HTTP_USER_AGENT']) && (strpos($_SERVER['HTTP_USER_AGENT'], 'MSIE') == true)) { ?>
I'm using z-index and I haven't see strange issues http://agec.ath.cx/lead maybe you could see a solution there
Web developer toolbar in firefox is a great tool to see CSS properties and change values on the fly.