The shopping cart is generally in a cgi-bin directory, or at least in it's own directory, not in your usual document root directory, so you either need to provide a path ro your CSS file relative to the document root of your site or include the full URL to it. Like this:
I use CSS extensively on this site www.smallfrypress.net on each page including the shopping cart and thank you pages. I used the complete URL (just as Loren suggested to you) and that has worked. Verify your folder structure, where you file resides and double check your spelling.
Thanks, but no, actually, that one page, I downloaded through FTP and tried to do the one by one! Just to see how it would look, but now I have fixed the custom templates so shouldnt they be overwriting the pages??