This can have a variety of reasons. Please make sure that the style sheet can be reached via the specified URL. Also, PDFreactor will only apply style sheets with the media type "print" or without media type. Style sheets with media type "screen" for example will be ignored.

When resources like style sheets are relatively linked and you convert the input document from content, make sure you specify an appropriate base URL so that PDFreactor can resolve the relative links to the resources.