When scanning multiple documents at once, the order in which documents are scanned differs depending on the ScanSnap model.
Documents are scanned from the document loaded at the bottom.
To save images in the order you want, load the documents face-down and top-first with the back side of the last document facing you.
Documents will be scanned from the document loaded at the top.
To save images in the order you want, load the documents face-up and top-first with the front of the first document facing you.