Thanks for the heads up, I did have a bit of an idea that they could be different as I had to make a crossover cable to connect the motion controller to the PC.

I hadn't realised there were two different straight through styles though, something to look out for!

It turned out to be the extended encoder cables that were the issue... I have no idea what I done wrong or why it might have caused it!

The software seemed to be receiving what it thought to be a good signal from the encoder but I got that run away on every axis... removing the extended wire from each one has fixed it! well... I have had each one working on its own, time to connect all three and see what issues I get next!

I also now have three exposed line drivers that will potentially get covered in coolant, so I need to sort that out as well.