Two things I would check/suggest. When homing the machine ensure both the left and right Y rail actually stall out on the front of the machine. I had a case where the right side would have about a 2mm gap after homing. I had to manually turn the right side to get it back square (you will need to turn off the controller or disconnect the stepper to turn the lead screw)
Second - look at this thread, there’s lots of good info on squaring the machine including diagonal measurements and what not.