"If you submit an ASP.NET Web page to a validation service such as the W3C Markup Validation Service, ASP.NET might render a version of the page that does not conform to XHTML standards. This is because the validator service does not report itself as a browser type that ASP.NET recognizes, such as Internet Explorer or Mozilla. When ASP.NET cannot recognize the browser type, it defaults to rendering downlevel markup, which does not include XHTML-conformant elements and attributes, or features such as cascading style sheet styles."
The article also discusses how to configure ASP.Net using a browser capabilities file to force it to render valid XHTML. I'll have a play with this tonight when I get home.