Strange Gantry Squaring/Homing

Hi - I've gotten Linuxcnc to work well on several machines but each time the machine wasn't constructed with enough precision to make it reliably work the way I wanted.  On this machine I finally built it the way I should have.  I used the files from my old machine and adapted them to this machine If something is commented out it is because I haven't got to that yet.  The machine moves great and the X and Z axis move and home really good.  The Y axis moves good but I can't get it to home properly. If things are set up so that each axis has a pnp sensor on side will respond to the sensor but the other side will turn off the led acknowledging it should home but it keeps moving towards the sensor.  If I tie both sides to a single side it works as expected.  This is fine but it prevents squaring.  I've included my files so maybe somebody could see where I've gone wrong.

Both joints of a gantry need negative home sequence numbers,
but your ini file has a negative and a positive:

[JOINT_1]

HOME_SEQUENCE = -3


[JOINT_2]

HOME_SEQUENCE = 3

Thank you for getting back to me. That had already been changed in the original file but I forgot to change it in what I posted online. It still has the same problem. Currently it is on joint 2. The constant homing issue has left the gantry a little out of square. It seems like whichever side is closer at the start has the problem