Hi again Nathan,
So we studied your shots. Very peculiar to us.
We see that the holes in the lines occur ONLY when the line are either horizontal or vertical.
Also we notice that the bold strokes are not continuous along the edge, they are sort of bulgy. That is not normal.
Could you help us with a small test? Do this:
Start with a clean project (New). Draw just one not too long stroke with the problem (hole) in it. You can undo lines until you get a small stroke with the problem in it. Then save and send me the .ap file! (niels at animationpaper.com) We can look at the data structure to see if something gives us a clue. Thank you!