Read QR Code from scanned PDF
The only reliable way to do this is to convert the PDF page to a bitmap, then using something like zxing to scan the entire page for the barcode. Extracting the individual images that make up the page won't work on every document: the barcode may be created using graphics operations rather than as an embedded image (that's how we do it), or if you PDF was scanned from a paper source as you've described, it will usually be one big image.
Once you've got the PDF converted to a bitmap, ZXing should be able to do this, at least in theory. Naturally I'd recommend sticking with us for the conversion to bitmap ;-)
If ZXing is having trouble finding the code, make sure it has enough white-space around it - you need 4 clear modules on all sides, so for smaller codes it should be about 10% of the width of the code in whitespace around the code, to help it scan.
Cheers... Mike (CTO@BFO)