Where does the processed.png picture come from?
Can you show us a step-by-step procedure to reproduce the problem?

It is a screenshot from the interface when you are inspecting the processed layouts (Manual inspection on Data Capture tab).

The steps to reproduce are as follows:

- Create new project from file
- Select missalignment-test.tex
- On preparation create 1 file
- Click "update documents"
- Wait for the documents to be created, and then do "layout detection"
- On the "Data capture" tab, select automatic and navigate to your project and select "DOC-sujet.pdf"
- After the process is done, click on "Manual"
- Change the view from "Original" to "Scan"
- Select pages different from the first and you will see the miss alignment on the detected boxes

Thanks.
The four corner circles must be at the exact same position on all pages on the subject for AMC to work. AMC should warn you if this is not the case, but here this warning is broken: I have to fix this.

Yea, I understand.

But the problem is that since it is the PDF shouldn't the dots be on the same position?

Also, the header is not moving them, is it? If you see the first page is detected correctly, but the next ones aren't.

On your PDF, the bottom dots are not at the same position on pages 1 and 2 (on page 2, they are lower).

Do you know what may be producing that?

As you can see I'm only adding the fancyhdr. Adnd that didn't create problems before, but now it is.

Any ideas?

Also, I'm not sure if that is related, but the detected layout at the per-processing detects all the marks correctly.

It is only on the scan that it produces error.

Do you know what may be producing that?

No but this is the source of your problem, and has to be fixed from your source file.

It seems to work with \geometry{headheight=3cm} in the preamble (the default value 2cm is not enough for your header).

Thanks for the help.

Indeed, updating the headheight influences the footer misplacement.

I will try to further investigate what is happening. It shouldn't be a problem whether the margins are updated.

For now, updating the headheight and the top margin fixes the misalignments.