With “landscape” do you mean the fancybox frame dimensions or the PDF page layout? If the first, then you need to adjust the size settings on Settings > Media under PDF. If the latter, then I’m afraid that is up to the PDF and/or the PDF viewer that is used by the browser.
There are some URL parameters you can use to pass commands to the Acrobat Reader browser plugin as described in http://partners.adobe.com/public/developer/en/acrobat/PDFOpenParameters.pdf but I don’t think there is a parameter that controls portrait/landscape display.
If you have a PDF editor and you can recreate the original PDF file, you should be able to rectify it within the PDF itself…
