Please HELP!  I am pulling my hair out…
I have been having this problem now for a while, but have been able to avoid it until now.  It seems that my Z-Axis is drifting or loosing steps.  What makes it more difficult to figure out is that it seems to be a math error of some kind as the results I can duplicate accurately.  
I am thinking this is a Mach 3 issue since I can duplicate the results.
Here is an example….  I am cutting a 3d part, I can let it cut the file out and when it is finished, it thinks the z axis is at 0.0, when it is actually at 0.25.  I can cut the part again after re-zeroing it and I end up at pretty much the same offset.  I am doing parallel finishing; I can see the bit is gradually and smoothly cutting lower and lower.  There is no big jump; it just seems to smoothly drift.
I can also zero the machine and toggle the head up and down about 15-20 times and will check zero and it will be off again.  I can do this at any speed setting and I let it completely stop before changing direction and I still produce the same results.  
This is what I have tried so far with no change….
Tried changing frequencies to 3 or 4 different settings.
Tried the shirline ½ step mode.
Tried setting the pulses under motor tuning to 5, then to 15, then to 20.
Tried changing the number of pulses per inch from 3200 (Setting I was running at) to 2000, to 1600, to 1000 and I still see the same results. 
I am running the Joes 4x4 hybrid machine.  You can see it here 
http://www.saberfire.com/gallery/Projects/CNCMachine/I am Running Mach 3 with the Hobby CNC Pro kit with the 305/oz motors.  I have the jumpers set to quarter step.
I am not sure what else to do here? 
Thanks,
Bobby