Relative links not working in Safari

Our web site has many PDFs and aspx files that link to each other. In a PDF, when we click on a relative link, the following message appears: Safari can't open "filename.pdf" because the first character of its address is not valid. When we loook in the error console for the page with the link, the warning says "Resource interpreted as Document but transferred with MIME type application/pdf." Our workaround has been to set up Safari to use Adobe Reader to open the PDFs, and everything worked just fine. With Safari 5.1, that is not possible, so we now need to figure out what the problem is. Thanks for any help you can offer.