Using updated test version of AMC (from Ubuntu ppa), xelatex engine, separate answer sheet, ovals for answer choice format arranged in 3 columns.
I have minor issues with question marks annotation.

If I select option Edit - Preferences - Project - Question marks position --- 'in the margins'
then first and second column of question marks are superimposed.

If I select Question marks position --- 'near boxes' then the question marks are switched around (marks for column 3 appear next to column 1 questions and so on).

This doesn't influence the scoring, marking and so on, the exam compiles and is imported neatly.

Best,

Niko Z.