I have a problem with my AR3 arm when it comes to homing

Specs:

AR3 Aluminium build

External encoders

Teensy 4.1

Teensy sketch 3.0

AR4 HMI 4.4

Running MK4 defaults

At rest before homing

J1 Dir 0v

J2 Dir 3.2v

J3 Dir 3.2v

J4 Dir 0v

J5 Dir 3.2v

J6 Dir 0v

When I home the axis, they all seem to home to the negative direction, for example J6 will home to the negative, if I change either of the motor direction or the home direction (hit save) it will still home to the negative.

However when I jog the axis, negative moves to the negative and positive moves to the positive.

This appears to be the same for all of the axis (haven't checked J5)

I have also tried loading teensy sketch 2.0 and AR4 HMI 1.3 (last known good) and have the same issue

Any ideas where I might be going wrong?

(2years ago when it was being used it was fine)