Couple of problems with the mod and CSS files.
1. If you store CSS as file it causes an invalid link which produces 404 errors.
2. It includes CSS files multiple times therefore leading to unnecessary round trips to the server.
I can demonstrate this with the reference implementation mentioned above:
http://last24tech.com/forum.php
If you look at the source you will see that it first includes
<link rel="stylesheet" type="text/css" href="css.php?styleid=2&langid=1&d=1321553 939&td=ltr&sheet=forumbits.css,forumhome.c ss,widgets.css,sidebar.css,options.css,tagcloud.cs s" />
This is from the regular template. Then, just before the IE6 Tag, there is this include, and I think it is coming from the mod. Notice that the order is somewhat different but the files are identical.
<link rel="stylesheet" type="text/css" href="css.php?styleid=2&langid=1&d=1321553 939&td=ltr&sheet=sidebar.css,forumbits.css ,forumhome.css,tagcloud.css,widgets.css,options.cs s" />
I think this should be fixed.