I was wondering if there was a possibility that the accel and velocity of the Z was too high. I ran some tests yesterday, one of them was simply to bring the tool down and zero it off the table as the new Z zero. Then I began typing in manual lines of code, just random G00 X Y Z movements all over the table. I then brought the bit back to the exact spot I touched off of and it was out 3 to 4 thousandths. I also ran a cutting program after that and the Z depth "drifting" was worse than ever. The material was 1/2" MDF that varied between .504 and .518. Some Z cuts cut all the way through and others left varying thickness of material left.
EDIT: If the table was actually the problem, the bit should have cut the proper break thru at the XY spot that I zeroed the Z, but by the time the tool came back to that corner it was leaving a thin skin of MDF as it made its pass.