Z axis incorrect

hello everyone

iv dusted off my old machine and am going to have another go at trying to get to know it better

with a few trial runs iv found that i am loosing depth of cut to what i have programmed. ie programmed to cut to a depth of 6mm but actual final cut was only 4.24mm

after a call to Russell (Epineh) he suggested that i first check the Z movement in mach to the actual movement of the spindle



i set the base of the spindle 55mm from the bed zeroed the Z axis and then lifted the spindle 45mm on the z counter on mach

that should have ment that the spindle should be a total 100mm from the bed, wasnt it was 89mm off the bed.

the machine is a 6040 chinese cnc

according to the specs sheet the ball screws are dia 16mm with a pitch of 5 mm

the motors are 387 oz motors from Homann supplies (with a lot of outside help i changed the moter rewired and fitter G540 stepper controlers to it)

the info/help i am after is what should the correct configeration be for the new setup, and were in mach do i change the settings

thankyou in advance for any feed back that maybe provided.

cheers Tony