Duplexing scan jobs 1 side is heavily offset

The offset on one side of the duplex scan printout is too close to the top and you loose a good section off the top of the document. I've performed the Tray2 alignment in Setup Menu, Print Quality, Adjust Alignment using a micrometer and I've got the alignments front and back as perfect as you can get them. If I print a reference page duplex, these do come out as perfect as I could expect. This tells me the image formation and print engine side is good .There will be a little skew from the path expected. But If I take the near perfect alignment test printout and scan it in duplex, one side is horribly offset near the top. I've ran the eDuplex alignment in the secondary menu if you know how to get there but there's no change. 
Anyone out there know of any other adjustments/calibrations that can be done to this scanner assy. I do service  for another major printer supplier and in their scanner service menus I can adjust all offsets manually as needed to ensure a good, equal image is obtained on both sides.
TIA

Sounds like there is a paper size setting somewhere incorrectly set. Is this a double side scan job (followed by printing, which should be easy to tell in the scanned result)? or a 2-sided copy? Check the paper size in scan or copy settings.
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