Problem with 404 pages in non-IE browsers

I’ve just converted my site to WordPress and I’m having a problem with 404 pages on non-IE browsers. I’m using a content negotiation script to serve up different doctypes and for non-IE browsers, the CSS is served up like this:
< ? xml-stylesheet href=”/css/master.css” type=”text/css” media=”screen” ? > which goes above the doctype.

That works fine for any pages that fall below /index.php, e.g. /index.php/fake-category/, but if the URL is something like /fake-category/ (or in my case, any of the folder structure from my original site – the pages that I actually want the error page to work for now), the 404 page appears but has somehow lost all the links to the CSS file, even though the source of the page looks exactly the same.

I guess it has something to do with the way the headers are being sent, but don’t really know enough about it to know where the problem is.