Maybe your subject file will help to diagnose.

Sorry, I'm still new to this software. What do you mean by the subject file?

The header/beginning of my source file is:

\documentclass[a4paper]{article}

\usepackage[utf8x]{inputenc}    
\usepackage[T1]{fontenc}
\usepackage[box,completemulti,separateanswersheet]{automultiplechoice}  

\begin{document}
\scoringDefaultS{haut=2, p=-1}  % correct score = 1; mz = max or zero (for single answer questions)
\scoringDefaultM{haut=3, p=-1}   % correct score = 1; mz = max or zero (for multiple answer questions)

When I scan the filled-in solutions sheet, the software detects all the filled-in boxes. However, the "show marks" button ends up showing a score of 0 and ? marks.

If it helps, here is my source file.

Kevin:

I suspect you are not following the appropiate steps after reading the scanned answersheets. Please tell me, step by step, what are you doing in order to process your test.

First, you have to move your questions inside the \onecopy{1} command.
Then, don't use the verbatim environment inside the questions, since it interferes with AMC. For simple code, you can use something like \texttt{code} instead. When verbatim is really needed, you have to store the verbatim content in a box and then use it inside the questions.

For the verbatim problem, see also verbatim inside questions.