No, this isn't 0.01" difference, it's 0.1" and it's always not cutting deep enough by ~0.1". I ran through some of the wizards and 1 out of ~4 times I was able to get a depth of 0.5". I did slow the feed rate down to 1 and that didn't seem to make a difference in the depth.
There is 1 controller board using Sanken SLA7078MPR driver chips which drives the Y, Z, and a slaved A axis to the Z (dual motors on the gantry). The Z-Axis is being driven by a TI DRV8825 on a different board.
Right now I have Z Axis motor tuning set with 4800 steps, velocity of 100, and acceleration of 10. I did have those lower the other day but today I went through the tuning again and played with the settings and the motor seemed to be running just fine at these levels. I used a feed rate of 5 and 1 in the wizards and that didn't seem to make a difference.
I'm actually cutting MDF (1 test I used plywood) so I would think that's about the easiest of materials to cut (short of foam and thin plastics). It's a 1/4" bit and most of the DOC are at 0.2" so I wouldn't think I'm stressing .
The X/A/Y Axis motors are NEMA 23 MotionKing 23HS8530-01A (3.0A, 1.8deg/step, 1 ohm, 1.8mH) while the Z Axis is a Nema 23 Sanyo Denki 103H7126-5040 (2.0A, 1.8 deg/step, can't seem to find the actual datasheet).
If you're still thinking it's missed steps should I lower the kernel speed to 25kHz and run 1 of the wizards with a feed rate of 1?