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.
Also, yesterday I ran the machine with the right hand motor running as a slave to the left and there was no run out.
I've not noticed any difference when changing the speeds.
I will change the Active state and report back.