Machs tuning will not help as it could only be the steps per unit were incorrect and if that was the case then the Y would be shorter or longer than it is meant to be. From what you are saying it looks like the axis is eventually getting on position but that it is slow to respond and Mach will have no effect on that as that is a function of the servo drives tuning.
The only possible things in Mach that I can think of that could affect things is possibly the Step active state is wrong for your drive but that seems unlikely with such a large discrepency.
Regarding ArtCAM, I am not sure how it could correct for that, if it was corner rounding then I could see it but seems to be a straight line at the corners that you are seeing.
Hood