For completeness, the PC has Intel Core2 Duo, 1.66GHz, 2GB RAM, And running Win7 Ultimate 32-bit.
I reduced the kernel to 25kHz and the Z-Axis speed to 30in/min, Acceleration = 10 In/sec^2
You're right, my bad in saying the delta depth wasn't 0.01", it is.
I'm still not measuring a depth of 0.500". Using my Mitutoyo Calipers to measure the depth leaves a little margin of error if you don't get the plunger and caliper 90 degrees to the wood. But even allowing for a little error in the measurement technique I still don't get the results I think I should be getting with this machine.
I still need to play with the pulse width and just for completeness, change the micro stepping to reduce the number of steps. I really would have thought that the lead screw setup on the Z would have given better results than the belt and pulley setup for the X/Y but maybe not? I believe it has an Acme screw on the shaft (need to look up what I order a long time ago) so backlash should be very minimal.
The saga continues...