Do you have a pulse time setting?
Yeah rising edge is correct.
What concerns me is the wiggle. I am still pretty sure you have backlash somewhere in your mechanical system that is causing the flats on your circle. The wiggle is the part that doesnt seem right.
The backlash is gone, so for now we’re now going to call this a multi axis interpolation issue which I doubt can be resolved. Changing the curve tolerance doesn’t make things better or worse.
I guess it could also be a potentially sloppy/out of spec preload on the linear carriages that may cause artifacts too.
Pretty disappointing nonetheless.
The backlash has actually only been reduced and masked by the new Gates belts and pulleys, even though it has improved it is still present measuring with an indicator again.
Anyone who has good experience with rack and pinion can suggest if trying this KHK rack and pinion system would be a waste of time or not? It is a tapered system. 
Seems like a logical advancement over a plain style rack system while being inexpensive and simpler than a split pinion system; just thinking out loud here.
Rack
Pinion
How much you measure? Have you thought about switching to the GT2 2mm pitch belts (the ones used on the SO3) and pulleys? The most backlash I was getting with those was 0.001-2" if I recall
Had the GT2 2mm pitch that came on the Pro (offshore brand) and the backlash was worse.
I feel like putting the gantry and carriage in the middle and tightening the belts from both sides is the better way to go about this? Otherwise there is going to be some slack.
The backlash repeatable in different locations? To roll out your presumable binding (aka grappy) areas - that could be causing skipped steps? Does the backlash look the same between X and Y?
The backlash is repeatable in the smooth spots of the X rails as well (Y is perfectly smooth). I haven’t detected any skips yet to date with these motors running at 48V and 2.03 amps.
I will need to measure the backlash on the Y axis again and get back with you.
This still sounds like something is not tightened properly somewhere.
I wish 
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Ordered some new laser goggles. Hoping these ones are way more comfortable and also safer. The current ones we have that cost more are definitely not comfy!
New goggles (Honeywell Flex Seal): G70108 Laser Safety Goggles
Current glasses (Frame #35): 35-245 Laser Safety Glasses
Maybe the circles will look more circular through a different lens.
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They aren’t rose tinted 
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I just read through all of @TX_diy’s comments in this thread tonight hoping to find a solution, as I saw the same issue with my XL Pro today.
I was trying to inlay a 1" circle of .03" veneer (cut on a Glowforge) in aluminum, and also saw the flat sides on the left and right of my circle.The little flat spot was just enough to prevent the veneer from sitting neatly inside the pocket, so I ended up making my pocket circle .002" larger in diameter.
I have a 1.5kW spindle, so the issue may not be because your laser does not provide a load parallel to your x-axis when cutting. I’ll play around with my machine some more this week and contribute here if I discover anything useful.
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Make sure your router is turned off and unplug it (Dont want it accidently turning on). Turn on power to your Shapeoko and connect to the machine with Carbide Motion. This should lock the stepper motors. Grab onto the spindle and trying moving it around. It should not be possible to move it without SERIOUS force. If you can move it, you have backlash. Take a look at the belts and stepper motors while you wiggle the spindle. Make sure to check the pulleys are not slipping on the stepper motor shafts.
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Oh man these things feel amazing! More eye coverage as well. 
They can also be used for CO₂ lasers for any of you curious of picking up a pair! (50% off right now) Hey, it can be a perfect excuse to have both a CO₂ and a fiber laser, you will save money by having one pair of goggles. 
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Here is one of the best videos detailing laser backlash and how there’s one type that has to be solved via software setting: https://youtu.be/DeCxeCrq0h4?t=52
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Where did you get them 50% off?
The link in my previous post: G70108 Laser Safety Goggles
The very option I need is grayed out and there’s no way to enable it.
