I'm having the same problem. When I use Preview to scan a multi-page document (using either the scanner's document feeder or one page at a time using the flatbed), with "Combine into single document" checked on the Preview scanner window, only the first page shows up in the PDF file created by Preview. I believe this started happening after upgrading to OSX 10.12 (although admittedly I don't scan every day so it may have started after an earlier upgrade) -- Preview used to create a PDF document containing one PDF page for each scanned page, which is the behavior I expect. If I use the "Open Scanner" button from the "Printers & Scanners" page in System Preferences, and scan a multi-page document (all other settings being the same as I set in Preview), the resulting PDF file contains multiple pages as I expect. I'd prefer to use Preview. I can turn "Combine into a single document" off, then scan each page into separate PDF documents, then manually add the 2nd and subsequent pages to the first PDF document (the one containing the first page), but clearly that's inconvenient and unnecessary, particularly when preview used to work the way I expected.