Joey,
What you are seeing is basically the loss of the microstepping when when the driver is powered off and then back on. This is normal, and you can't really do anything about it, except:
First, don't power off the motors with the driver board still under power, you will smoke your board!
Second, you can install home switches. This is really the only way to be "Hans off" accurate. But, don't use a mechanical contact switch. You should find an optical sensor or switch that has really tight repeatability. Like in the microns! Switches will vary a great deal and since you are dealing with your diameter, a half a thousandth means a full thousandth on your work.
Third, there is a board that uses rotary encoders and works with Mach. Basically, it creates a second DRO that runs behind the scenes, and it compares it to the Mach DRO at all times. You can control the variance before a default, and it will let you return to your actual position. It's great for missed steps too. It does relocate your motors on start up! However, you have to add encoders, it doesn't account for any backlash in your lead nuts, it doesn't account for histeryses (sp?) in your bearings, and it costs a little bit too.
What we do is to make a cut, measure it, and adjust accordingly. It doesn't take that long, and it ensures that everything is right. Even if I had a servo system, I would still be checking parts! I just don't completely trust them. Things happen! Parts move!
Hope that helps!
Royce Bunnell
www.obcues.com