Yes that is “working as intended” because stepper motors also work as generators. So when you free move the gantry the stepper is generating voltage.
Because the Y motors are wired together in reverse they start to power each other.
So when you free move them fast enough they act as a break.
It also puts power back into the gshield which can make the leds light up and other strange things happen. (In my case it can trip the spindle on relay - scary!)
It is unknown if this can potently damage the gshield or not. So most people try not to move the motors too fast by hand.
It should not be a problem when the motors are being powered by the gshield as they are both being powered at the same time to work together.
That is tricky.
Your best bet is to see if anyone who has independently powered Y motors will do some test runs at your acceleration rates and see if it can handle it. That will let you know if changing the controller will make a difference.
But you will have to spend a little $ to make a change.
If you are comfortable with soldering electronics yourself you could wire in a 4th stepper driver chip.
But unless you are comfortable with that level of modification and have a lot of the necessary boards pins and wires on hand already you would be better off going with something else.
Here is the cheapest 4 driver option I have seen at around $60
GRBL shield alternative.
But if you do wind up spending $ on this I would take a hard look at if S curve acceleration will help. Saving $100 won’t help if it doesn’t fix the problem.
Read up on acceleration curves. You may be approaching the max acceleration of the motor. I know if it goes too high the motor can’t keep up and will start to miss steps. But how high is too high has to do with the motor torque rating and gearing ratio on the axis.
(I think the Nema 23’s in the kit are 140 oz-inch)
But I guess if the X axis is handling it then it is not a motor torque issue as they are the same motors on the same gearing.
If it is just the Y axis (and you checked that no V wheels, belts or pulley set screws are loose or too tight) my best guess it is the motors being tied together and at those high speeds the reverse current being generated (usually not enough to be an issue) is starting to be a problem?
How big of a project are you working on?
If you are doing lots of BIG moves you may not need a huge acceleration.
Acceleration being how quick you get to max speed.
If you are doing all 12 inch moves does it mater if you are getting to max speed in .08 inches instead of .01?
What if you just try the higher speeds without the high accelerations. Yes you won’t actual be running at max speed 100% but that is the only adjustment I can think of without moding the machine.