Have you been able to duplicate the stalling with the voltage meter attached?
Try combining one of your Y motors with the X, and one with your Z motor controllers.
Since you have both Y motors on the same power supply, when that axis is decelerating, both motors are inputting voltage feedback to the power supply. By splitting the two motors across both power supplies, the other controller and motor are acting as a load, helping to reduce the feedback on the power supply.
The last few paragraphs in this article describes this exact issue.
https://www.geckodrive.com/support/s...ly-basics.html
One additional thought... I believe that your power supplies have a +/- 10% adjustment via a small pot. Try dropping the voltage 5-10%. This may drop the voltage being fed back just enough to avoid the protection circuit from tripping in the power supply. This does affect the max speed of your steppers, but who cares how fast they can go if you are throwing away failed projects due to this issue. I have no evidence if this will work ornot, but is certainly worth an experiment to see if it has any effect.
I hope that this helps.
Thanks, John Z
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