If you are running Win 7 64bit, you must install the "Adobe PDF iFilter 9 for 64-bit platforms" patch. Without this patch you cannot search for OCR'd PDF's on your PC. Basically, the ScanSnap scans your document, and then the ScanSnap software uses OCR (Optical Character recognition) to turn than scanned paper into a PDF that is searchable. Well, without this patch, Windows cannot extract the text and index it, making it searchable in Windows.
You can download the patch here.