In the in-game finetuner menu, the X and Y axis are global, but Z is relative to the part's current rotation angle and it depends on the X and Y angles, so when you set X or Y close to 90 or 270 degrees, two of the sliders actually control the same axis and one of the axis can't even be controlled.

This is utterly annoying and I'd be very grateful if the devs could fix this :)