Very mysterious dropping steps on one Y axis motor...I'm starting to lose it!!

[JAZZCNC]

This is brilliant! Thank you guys
I have been checking the discrepancy by measuring the distance from the end of the track to the carriage when the toolpath has finished.
The discrepancy increases the more complicated the toolpath is so that would back up your advice.

You need to do this in a methodical order. First, you need to identify if you are losing steps because of pulse timing problems or tuning/power/mechanical problems.
Forget your toolpath and just do the bounce test first by making a simple G-code program to move the axis back n forth, this will tell you straight away if it's a pulse timing issue and if it's not then you can move on and look else were.

Also, yesterday I ran the machine with the right hand motor running as a slave to the left and there was no run out.

Ok, you are giving confusing messages now.? So are you saying you were not using slaving before.? If yes then how were you doing it.?