Afterthought: you problem reminded me of a recent post :
the reason was a miswiring at factory of one motor connector (two wires were swapped). I wonder (this is far fetched!) if maybe one of your Y motors is wired correctly and works ok, while the second Y motor would be wired incorrectly, and produce this sound (but since your gantry IS moving, that would mean the OK motor would still have enough power to move the gantry fighting against the faulty motor…told you this was far fetched). Anyway, my point is, check whether the wire colors are in the same order on each motor connector at controller side, to at least rule out this possibility.