This is an interesting one, I've had this kind of pattern before. I admit, my standard response is delight, because this is an artefact of the nature of the machine, and that's really the appeal of the machine (to me, as an artist, er an "expresser"). I imagine this could be frustrating as a draftsman though 🙂
I think you're right that it isn't a homing/measuring issue.
When I've had to track this kind of thing down (corners being knocked off things), I've usually improved the handling by doing something with the gondola, and I've diagnosed issues by carefully watching the angle of the pen during the drawing.
When the pen changes direction, there is always a moment when the gondola moves (a cord is being pulled), the gondola pivots around the tip of the pen, but the pen doesn't actually move against the surface of the paper. In a perfectly frictionless, perfectly balanced gondola, then even the tiniest movement of the motors translates to a line being created on the paper. This is impossible in practice.
If you see the gondola pivoting around the tip of the pen, then pull the pen in a little bit so the only the very tip extends out of the gondola. Alternatively, you can add some extra weight to the gondola to make the whole thing more taut, but of course there are issues with that too (eventually will have to add more weight to the counterweights, eventually need more power to move it all etc).
Paper surface makes a difference - rough paper increases the friction. I believe that speed makes a difference - but I can't decide how! Moving slowly gives more opportunity to get stuck on rough surfaces, where fast moving will skate over it. Alternatively, slow moving gives more opportunity for gravity to pull the V taut and overcome the friction of moving the tip on the paper, and fast moving causes the momentum and inertia of the moving gondola to skip over subtle detail. Those are guesses, intuitive thoughts rather than anything based on experiments or reality!
I also have solved a problem very like this (a grid where the machine drew each cell individually) by changing how I created my artwork. I used the pathfinder tool in illustrator to convert line art into vector art, and ticked the box to "prefer straight lines" or something like that.