I think you made some small errors in your source file.

• remove \AMCformBegin and \AMCformS calls. They are not to be used in your case, and are not needed here.
• \examcopy{800}{ ... } should be \onecopy{800}{ ... }

Maybe these errors disturbed the scoring process...

Try one of these:

1. Make a backup (zip file with all content) of your project directory, correct the source file and re-run marking (with Update marking scale box ticked)
2. Try to build a new project from the corrected source file. If the subject looks exactly the same, you should be able to process your scans with it.

I solved it! It seems that the included tabularx in the latex code was the culprit. Not an obvious troublemaker.

Anyway, thanks for your suggestions. They made me rethink the problem solving path.