So at work we have had this issue with only certain PDFs showing up in the search results. It had nothing to do with what directory the files where in (I tried that). It had to do with what version of Acrobat they were saved as. So here is what I found, the PDF IFilter v5.0 which we installed to index our pdfs uses the pdf 1.4 protocol. However when you save a document as Acrobat 6.0 it uses the pdf 1.5 protocol. Unfortunately there isn't an updated version of the IFilter yet and the "current" version was last updated in 2001. So if indexing services isn't cataloging your pdfs, check what version they are.
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