Long story short I just ended up assembling my X-Carve (1000x1000) and following the wiring test, X and Z axis worked fine, nevertheless as soon as I try out Y axis the machine stop working and disconnect the X-Controller without allowing me to move any of the axis again.
And use BLUE LOCTITE!
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at first thought would be that the y axis motors are not hooked up correctly and there is some sort of shorting going on resetting the board.
Try a different stepper motor on that Y-driver. Could be a short/inproper connection/defective driver/defective motor.
Swapping out the motor with a known good one can rule out some of the potential failure points 
Try using a better USB cable. Look for one that has braided shield and ferrite beads, but shielding is the most important factor. This one works great for me: Amazon.com
I had dropout issues with USB using the original cable anytime something AC would turn on in my shop.