I agree with Roger.
Your Gcode works but is not good Gcode.
As the circles are created as two semi-circles Mach3 makes a slight pause between each and flex (maybe in the machine, the spindle, the endmill, etc.) is creating two knibs in the machined toolpath. I think this could be improved, as would the roundness of your holes if you slowed the federate down further.

Tweakie.

Checked gcode from previous runs on my old machine setup.  Absolutely identical… the only things changed are the linear guides and clearpaths…

Fusion360 has gone quite a bit of updates… but the output gcode is relatively the same.

One thing I noticed when doing test cuts (larger circle in the pics) is that the little bumps are the same where ever I moved on the piece of acrylic.  It's like it's cutting half arcs with little bumps enter and exit to the contour base it's direction in the routine.  It's does a bump when it begins to travel from left to right and then again right to left on the x axises.  I've double checked all of the mecahinals of my machine and nothing was loose nor did the rack and pinions have backlash...  So stumped.  Next steps is to redo my tuning of the clearpaths.  Thanks you two for helping me through this while I try to find the root cause!

Look at this edited pic.  This is what you referenced as well tweakie... which occured when I reduced my feeds from 1200mm to 500mm. 

>  nor did the rack and pinions have backlash...
With all due respect, rack and pinion always has backlash. Sorry, but that is how it is.

That is why we use ball-screws. Mind you, even a ground ball-screw with double ball-nuts will have backlash, but it will be sub-micron and beyond my eyes.

Cheers
Roger

Fair enough… im just going by my experience with what i have as a machine and similar gcode used with no issues previously.  Im engaging in the avid forums as well on clearpath tuning and it possibly could be that and how there could be a contention between the clearpath servos and mach3 controlling the motors.

Thanks!

Something that I omitted that I want to get your opinion on.  My Y axis is running two Nema 34 servo and my X is running a single new 23 servo. Prior I was running all three motors, two on the y and one in the X, the same. Could not having the X axis motor match the Y motors cause this issue? Thanks.

Not enough detail. What sort of Nema 34 servo: stepper or 'analog'?
Do the motors have integrated gearboxes?
What sort of (electronic) drivers?
Yes, lots of detail needed IF you want high performance.

Cheers
Roger

I just want my circles and arcs to not be rounded squares.

The setup:
MM is my default units
Ess with c82 bob
Clearpath sdsk nema 34 x 2 for Y
Clearpath sdsk nem 23 form X
Both have internal drivers
Im using avidcnc’s rack and pinion system. 
Nema 23 has a 3:1 gearing reduction
Nema 34 has a 3.2:1 gearing reduction
Both servos have no microstepping defaulted to 800 steps (units) per revolution.
Both gearing are 20 tooth per 25.4 mm (1”) rotation
Hope this helps.

Thanks!