Auto gantry squaring issue

[NeeqOne]

I have finished wiring up my AXBB-E. Everything seems to working. However, the homing has not been that smooth. Initially, I had the NPN NC inductive proximity sensors for the X,Y and Z axes connected to one isolated input and the A axis which is a slave of Y connected to a different input. However, homing did not work with this set up.

Currently, I have wiring all the sensors to different inputs. X and Z now home correctly. However, the Y axis do not home if the A axis limit switch is connected to a different input. It only homes when both Y and A switches are connected to same input. I wanted to have Y and A on different axes to help with squaring the Y axis. I don't know if I am doing anything wrong.

I have attached a copy of my profile.