it does sound as John rightly suggests that it could be the z axis motor not being powerful enough for the job , give us details of the stepper motors used , and the machine you have converted , or even a photo will help , and no doubt we will be able to help further and solve your problem.
also does this 2mm multiply each time ? i.e it becomes additive to the measurment before , or is it consistant on each movement of only 2mm , if so this would indicate
more of a backlash or axis screw / nut movement
also give details of your power supply ? , it could be you are just not supplying enough voltage or current specificaly to the z axis motor , as this is usualy the most demanding axis , having to lift the weight of the head etc .
Dave