Please send your project directory with your scan, unless I'm afraid I won't be able to understand what's going on.

I figured I wasn't giving enough information -- I don't know the program yet so don't even know what to tell you!

See attached.

Cheers!

Thanks. On the scan, we can see the two top corner marks (circles), but not the two bottom ones. AMC needs the 4 marks on the scan to be able to analyse it.
Perhaps you don't use A4 paper? If so, edit the first line of the LaTeX source file:

\documentclass[a4paper]{article}

Yes! That solves it:

I've replaced [a4paper] with [letterpaper] and scanning now works.

Cheers!
Devin

And thanks for the very quick assistance!

Yesterday I saw something similar: 2 of my 8 paper ballots, scanned for faster speed in a 90 degree angle, were not auto-rotated by the Fujitsu scanner driver. AMC 0.550 (yes, stock Ubuntu installation) refused to recognize these two. Some I thought I had read that AMC would not mind about the page orientation, but obviously it does - right?

It should handle the 90° rotation automatically with a recent version.
You can install one easily on Ubuntu using one of AMC's PPAs (see for ex. this one)

Brilliant, exactly what I needed!