To enable automatic rotation on your scanner with any software application, use Kofax Virtual ReScan (VRS) Professional. It not only does auto-rotation, but can do a whole range of image enhancement while your scanner is scanning in real time.
VRS must be compatible with your scanner, and you must get the version of VRS that is for your scanner. You can find the list of compatible scanners and the VRS version needed for each scanner here.
There are 2 types of VRS as well, Basic and Professional. Kofax VRS Basic does not include Auto Rotation or Advanced Clarity and lacks the automatic color detection, hole fill, and blank page deletion features found in Kofax VRS Professional. You can find a more in-depth comparison of the Basic and Professional features here.