Is your Y axis dual-motor? Is it happening in the same physical place each time, or do you mean that the files that cause it always stop at the same line of gcode but in different physical positions?

I have a dual-motor X axis, and the only time I get the problem is when, for some reason, the gantry has gone out of square (and it doesn't seem to need to be far out). Curiously, it happens at the same place along the axis, presumably where the rails aren't quite perfectly aligned, around half-way along. The only other time it has happened was when I was tuning the system; if I pushed things too far (speed or acceleration) I could get stall events, but they don't happen now that I have settled on the parameters I am using.

Assuming no squaring problems, can you wind down speed and/or acceleration to see if that helps? If so, it might provide a pointer.