If you are running at maximum speed, and it happens in manual and CNC mode, I have seen this.
Reduce the maximum speed slightly.
Whether the machine is reading the front panel pot or the CNC pwm, the a/d converter overflows if input signal is too close to rail voltage,
causing the converted value to wrap to a small value.
Software bug. Little chance of fixing the firmware that causes this.
In CNC mode reduce your maximum speed slightly until it works reliably regardless of temperature and supply voltage.
For manual mode, put a preset potentiometer, 1K would most likely be OK, in series with the clockwise end of the pot. This allows you to reduce the maximum output of the pot.
I was not able to check the PCBs when I saw the fault, so I am not sure if any adjustments are possible.
If you find a circuit, (in your wildest dreams), post it, and I will know for sure the easiest way to fix this.