Which version of AMC are you using? Also can you upload a sample tex file which illustrates this problem?

version: 1.2.1463
OS: MacOSX (installed by port)

I am preparing a light version. Before that I try on a debian system to see if the problem persists.

I found the problem!

In the preamble I was using the command
\geometry{a4paper,inner=2.7cm,outer=1.3cm,twoside,top=2.5cm}
to move the whole text a little on the side. Indeed we print a booklet on A3 paper which is stabled in the middle and, after correction, it is cut neatly.

On mac I did not get any warning during layout detection.
When checking on a debian system, I got a warning saying

"Some potential defects were detected for this subject. Correct them in the source and update the working documents.
The corner marks and binary boxes are not at the same location on all pages (See for exemple pages 1/1 and 1/2). "

I've set back the geometry to a centered one:

\geometry{a4paper,hmargin=2cm,top=2.5cm}

(note that the total width is exactly the same).
Everyting is now working as expected, even on MacOSX. I since the width is the same, I can scan the exam without issues.

Best regards
Simone