Why is Doxie Pro outputting my scanned papers out of order?

Doxie Pro is designed to keep your documents in the same order, on the way and on the way out of the automatic document feeder. If the order isn't the same, you might have your Direct Feed slot open (which is just for a specific kind of scanning) – you should close it when you're not scanning with the Direct Feed slot.

Here's a video with a more detailed explanation.