ok, so it looks like the encoder was faulty, I've now changed the encoder and index homing is now working.....ish!
Now I have a new problem, The machine doesn't home in the middle of the Y Axis anymore. My thought is this is becuase the new encoder has a different number of pulses per revolution compared to the old one. The old one had a 1250 PPR. This is my new encoder, (which is the same as I use on my z axis, which works perfect)
https://www.cui.com/product/resource/amt10.pdfWhere in the software do I change the PPR to the new figure, I assume is 2048 ppr?