The cropped scanned image is different from the original document or not cropped at all.
For scanning flat documents:
Modify in the [ScanSnap Manager - View cropped images] dialog.
In the [Paper] tab of the ScanSnap setup dialog box, select the same size as the document (standard size or custom paper size) in [Paper size].
For scanning double page spread documents such as books and magazines:
Modify in the [ScanSnap Manager - Book Image Viewer] dialog.