This could be a simple bug in the application, but if the document comes upside down, then simply put the document in the upside down mode and the scanner will provide the correct orientation. It also depends on the way you scan the documents. If they're images, then right-click the image and choose Windows Preview, then you can rotate it using the available buttons.
Or you could use an image editor like XnView to rotate the image: http://xnview.software.informer.com/
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