CPR and PPR can mean the same, I have seen all sorts from different places and it can get quite confusing.
As I said your Z we know has no gearing and you know the pitch is 0.1inch
So to move 1 Inch you need to rotate the motor(and screw) 10 times.
As you have the Steps per in Mach at 10,000, and I presume when you command a move of 1 inch it moves 1 inch, then that means your encoders are 1000 pulses per rev or 250 line. The only other factor would be the drive, if you had it set to 4x that would divide the pulses required from Mach by 4 so that would mean your encoders are actually 1000 line 4000pulses per rev.
So double check the drive setting and make sure you dont have it set to 4x.
Hood