Well, It's probably me being stupid!!
1 of the motors was spinning the wrong way.
I tried reversing the wires which made Mach wrong and the motor right.
Swapped it back and set that axis as active high and it was fine.

The easy way (likely the proper way) I've now found is when you set up in your soft limit screen just click "reversed" and job done! Duh!!!!
Only took me 2 years to spot this