I believe you may be seeing the effects of a long-standing bug in Mach3. If you have two axes in-motion, and then transition to a 3-axis move, the acceleration setting of that third axis will be ignored, and it will be expected (more like required) to accelerate at the same rate as X/Y. This can be easily demonstrated by setting your Z axis accleration to a very low value, as compared to X and Y, then doing a move that transitions to a helical move in X/Y/Z. The Z axis will lose position at the entry to the 3-axis move. This is a known problem, and will be fixed someday, but it's not high on the priority list. This gave me fits when my mill was capable of 3-- IPM on X & Y, but only 50 IPM on Z. At present, the only work-around is to run in Exact Stop mode. It would not surprise me a bit if there were a related problem occurring when moving a rotary axis in concert with linear axes.
Regards,
Ray L.