I have a Shapeoko 3 XXL with Z-plus, Carbide 3D router head, sweepy V1 dust boot, BitSetter and BitZero 2. When cutting jobs with multiple bits there will be height differences in the depth of cut between the different bits.
I use Vcarve Pro with the multitool post processor for shapeoko. And always use Carbide Motion to send the job to the CNC. I usually design in illustrator and import the vectors to cut. I have seen this happen as well with the same bit during clearing will cut deeper close to the vector but slightly higher clearing out the rest, no bit change in the gcode.
I have checked level multiple times as well as calibrated the stepper motors several times. Nothing is loose. Bits are tight in the collet. I have also tried using Carbide create as the software to create gcode. It seems very inconsistent as to how much difference to sometimes none at all.
The fist photo is the most recent cut. 3 bits. Nomad #201 1/4" upcut, Freud 1/8" down cut, and Amana Tool 1/16" down cut.
Second photo one of the more extreme cases. I believe this was the 1/8" Freud down cut doing a clearing pass before the tool change. Each path cut at a different depth.