Does anyone know why I get a situation where AMC appears to sort the boxes incorrectly?

I have the following settings:
DPI: 200
B&W conversion: .70
Force Conversion: checked
Marks increase: .20
Marks decrease: .20
Default darkness threshold: 0.50
default upper darkness: .70
box proportion: .75
process scans with 3 marks: checked

The zooms however, show the filled in boxes (most with a darkness score of 1.00) sorted as unchecked (see attached). MSE and Sensitivity are also not marked as problematic.

Any ideas about what is going wrong or how to fix it?

Thanks!
D