IIS 6.0 404 Redirect to pagenotfound.aspx themes missing

OK here is the issue. I have IIS 6.0 set up to redirect missing pages
to pagenotfound.aspx. I have asp.net set up in the web.config to
redirect missing pages to pagenotfound.aspx. I am using master pages
and themes. I can not make any changes to the paths of the css files
as those are in the head control on the page that is generated from
the mystical land that is Microsoft.I test that these are working by
going to pages that do not exist.

Say I have a directory that is

www.mysite.com/test/forms/test.htm.

This test page exists so everything is happy. Now I put in

www.mysite.com/test/forms/test2.htm

this page does not exists so it redirects to the pagenotfound.aspx.
And the world is a wonderful place and things are great.....

Now I try the same url but add a directory that doesn't exist.

www.mysite.com/test/forms/a/test.htm.

Now here is the problem. The site still redirects me to the
pagenotfound.aspx but the page no longer renders the css in the file.
What the real kicker here is that the page that displays and works has
the exact same source as a page that displays and does not work. But
the two pages are different. I can show you examples of this if
someone is willing to help tackle this one.