When you send the machine to zero on Y axis (problematic one) and it stops without turning confirmation light on, go to diagnostic number 801 for Y (button DGNOS, page up) and check if reading is bigger than the value of parameter No.71 (in-position width). If so, push reset, go to JOG mode, move the axis minus and plus observing DGN801. Note the mean value and adjust parameter 125, so when moving machine DGN 801 is close to zero.
After that check again reference return.