Same thing was happening to me, and I found out it was because I had a muckaround site. In technical terms my blog’s home resides at site.com/wp and I had the site I fool around with at site.com/wpmuck so i could change things without breaking them, the problem is, the varible in index.php refers to:
@import url( <?php echo $siteurl; ?>/wp-layout.css );
$siteurl is being pulled from whatever you set the homepage as during installation/setup, so it’s still taking the stylesheet from the directory of the site you don’t want to break (the unmodified .css) All I did was rename /wp to /wpBU then renamed /wpmuck to /wp and everything worked, if something breaks you can just rename the directories back and you shouldn’t have a problem. Hope this helped.
