Optical Registration issues

I’m scanning 12 Field Inks into Animate Pro and I’m having some issues with Optical Registration. My scanner in a Brother MCF 6490CW A3 feed scanner. I’m scanning in sideways because that’s the only way the paper fits. Optical registration is working when the setting is set to “Bottom”, but the drawings aren’t rotating properly. The peg holes are still on the left of the screen and the drawings are rotated 90° clockwise. I’ve got a lot to scan and I really don’t want to have to rotate EVERY drawing and layer.

-Animate Pro, Mac 10.6.8, iMac.

You could just attach a peg layer as the parent of all the drawing layers, and rotate this peg 90 degrees in order to achieve the correct rotation.