A couple of updates:
First, everyone having this issue should submit feedback to Apple at http://www.apple.com/feedback/macosx.html You won't get a direct response, but the more bug reports they get, the more likely they are to take notice and fix it.
I tried scanning as a multipage PDF using the flatbed scanner instead of the sheet feeder and got the same result.
I found a fairly easy workaround: Importing a document as a multipage TIFF document does work. You can then easily export this as a PDF. When I tried this I found what appears to be another bug in that the first page/face shows up twice, so a 3 page document would actually have 2 page ones and end up as 4 pages, but you can very easily delete the extra page one and be on your way.
A second workaround is to open the Image Capture app and import from the scanner this way; I tried this and both multipage TIFF and PDF scans appear to work as expected.