I have a similar machine setup on one of my machine. Other than a rack an pinions getting tightened up, the spindle being supported at the top, causes deflection as you are cutting. You will see it more if you surface something. That is the only way I caught it was when I was surfacing my spoil board. The only way around it is to cut slower or shallower, unless you want to get into lowering the gantry. Now your setup up may have something totally different, but on mine with the spindle being supported that high up caused crappy finishes.