Stepper Motor Control Error ASD30A-A

I am not 100% sure this is the correct forum for this, but it seemed the most appropriate

So I am running into an issue with a retrofitted ShopBot. It uses 3x ASD30A-A Motors from Oriental motor, with combined Encoder/controller. Additionally, I replaced the control board (Which was USB based) with a Mesa 5i25 and 7i76.
Now the company uses it to do some scientific testing by passing an instrument back and forth across one axis (The one we call Y) quickly, and X and Z move very slowly.
For a long while, it has been working fine, until recently, one of the technicians who uses it noticed that in the Y direction (Our 'Fast' direction) at 750in/min when the robot moved Right to left, it would behave fine, but when moving left to right, it would make a weird beat frequency while it moved, instead of a steady whine (somewhere around 5Hz-ish), and then it would not smoothly decelerate and instead brake suddenly when it got to its intended end point, causing a bit of a clang and causing the instrument mounted to it to vibrate.

Now, today, this has deteriorated further. Now, instead of just making everyone a little nervous, when it moves in one direction (Right-to-left) on its return path, the motor stalls out giving us a nice cryptic "Speed Error Protection" message using its blinking alarm. It still has no issue moving left-to-right. I have been fiddling with the filter on the motor controller and tried adjusting the acceleration to see if it will go away, but it won't. The controller/Motor manual recommends that I "reduce load", however it is a load it is able to handle at least in one direction, and has been able to handle it in the past. The machine is only a year to year and a half old. I have found that if I increase the speed too much, it gives the same error. I have the controller set up such that it receives the pulses on the same signal line in either CW or CCW directions, and I just set the direction control High or Low depending on which direction I want it to go in.

Finally, if I reduce the speed (750in/min to 600in/min), the problem appears to go away completely and I have no asymmetry between right-to-left and left-to-right movement, and it doesn't throw a fault.

Does anyone have an idea why I am getting this asymmetric behavior? Has anyone seen this type of behavior before? I am stumped as to where to look.

also check any ballscrews and bearings on the shaft and couplers . for any binding

I figured it wasn't LinuxCNC, rather some of the later parts that interface with it, I just didn't know a place to ask besides this to find out if anyone has had a similar issue with a motor before.

Any ideas how to test for this kind of thing without dismantling the motor or encoder? I'm hesitant to do so, as I am not good at reassembling mechanical things.

I am definitely seeing an increase in likelihood of the issue as I increase the speed past a certain point.