This really is a continuation of Hoods comment -
Are you making allowance for the diameter of the cutting tool instead of the radius. If your dimensions are the same on Mach 3 e.g. the pockets are 1 inch square, and the inlays are one inch square, then to get the pockets consistantly short, and the inlays consistantly large, it would seem that the code is making allowance for the diameter of the tool and not the radius.
Hence it makes too much allowance.