Try making the PDF a different way. Use the Adobe PDF printer if you were using Mac OS X' built in PDF creator.
I had this same problem. The live chat helper couldn't help me, or said they had to look into it and it would take 24-72 hours. So, I tried a few things. This is what I did.
My original files were created in Microsoft Power Point. Only some of the documents I created weren't letting me add numbers, headers, or footers. So, I opened Apple's Key Note (Apple's version of power point). Saved the document as PDF through Key Note. AND problem solved.
Hope this helps someone!