I have experienced same problem with some extensions (originally with mht)
http://www.kinook.com/Forum/showthre...ight=Keyworded Very often too with pdf.
I've realized that the software or method used to generate the pdf document is what causes this issue (if the document is generated by some applications other than Adobe Acrobat for example, or by using the Print command from most programs).
I currently have many faulty keyworded stored items with few keywords, many pdfs. I hope very soon there will be a way to efficiently re-keyword many items in batch, as this issue impacts the search feature negatively. And I don't have plans to purchase Adobe Acrobat (proprietary pdf document maker.)
Leoram