Mis-homing is my first reaction too. It sounds like the cords are a little shorter than the machine thinks they are, so maybe your home point is physically a mite too high. Quick test can tell you if that's true or not though, so I guess you've probably already tried it.
Is the top line horizontal and straight?
There is nothing linear about this kind of machine, and as the angles from the spools change then so do the tangents of the cord and the effective width of the machine. The area in the middle is a lot more regular, but it isn't a big area. Could it be that you're drawing very close to the top edge of your machine (near your sprockets)? All the rules break down there, it's like the badlands of a polargraph machine - keep away from it.
This is a reason I don't draw rectangular borders around pics 🙂
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