If by reversing the cut the part comes out undersized. What would that imply?
reversing the direction of the cut would indicate flexing of the gantry/z axis or any other distortion due to the forces on each piece being reversed....
I've noticed this to on my POS machine that uses plastic pieces as structural elements...I cut a LOT of letters and when I cut clockwise it cuts fine...when I cut in the opposite direction, it takes off about .01 more....It's not in my design software, it's not in machine code error, it's just a POS....so what I have to do is have a separate tool for reverse cuts....ie: I use a .125 down cut spiral for the initial clockwise cut...and then "lie" and use a .127 for the reverse cut.....I still use the actual .125 bit, but I tell the software it's .127 in diameter.....
I do two passes because I cut a LOT of pine and in one direction: the bit doesn't shear off the fibres cleanly in all areas so a counterclockwise takes care of them...saves me a LOT of sanding.....