Ok, I think I figured out your dodgy corner/rounded corners. Your program is set up to make a rectangle, with the only radius being the diameter of the bit you are using. The controller for mach3 gives you a nice button for changing between exact stops and constant velocity, the trick is to find the sweet spot to keep the machine from just stopping at the corners, and the machine skipping the corner for speeds sake. Needless to say, if you want a rectangular piece cut out, something with rounded corners will not suffice. Try running this same program with that button set to dwell instead of CV mode. (This is also the reason for the bottom left corner having an extra cut spot. The machine went to the corner, plunged, then started making trips around the perimeter, rounding off the corners, except where it initially plunged, since it started at the corner instead of skipping that corner spot. So you can see where it came up short connecting that cut). I believe mach3 allows this parameter to be set with gcode, you could try opening the gcode in a text editor, entering g61, and seeing what you get. For my old janky router, I'd set g64p0.015, which would allow the machine to skip a point in the code by 1.5% (or maybe it was 15%? I forget how the p factor actually works), which would produce smoother curves without causing such large radii.
It also looks like your acceleration is set too high, or you're pushing the machine a little too hard. Those scallops on the top side of this picture are from the bit either slowing down due to too much load, or from deflection in the bit. I forget where the page is, but you can bring up tuning for each motor easily. Shoot some pics of that info and post here.
Also, was this a kit, retrofit, or an assembled machine? I'm just curious. The control box has some great connections, props if you did all that!
