Out of the box index server won't index .PDF files. I have exactly the same issue while implementing a search solution at a solictors I was working for.
The solution, there's a download available on the adobe site that, when installed on your IIS Server will allow for the indexing, an so searching of PDF files.
The official line from Microsoft:
Microsoft Index Server versions 1.0 and 1.1 do not index Adobe Acrobat (.PDF) files.
Adobe is working on the IFilter for Microsoft Index Server.
Adobe have actually worked and finished the IFilter, here's the link to it:
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