Z Height Issue

I recently finished my Prusa I3X build (my second printer), and it seems my Z axis is not moving the correct distance. I used the calculator at [prusaprinters.org] to find the steps/mm (unit) for my printer (it was the default 4000 for Z) I am fairly certain I have a M5 X 250mm threaded rod.
When printing an object that should be 25X25X25 I get an object that is 25X25X18

My best guess is that the motors I am using are 0.9 Degree instead of 1.8, how would I check this?
Is there another way to calculate steps/mm?

If you are using 1.8 degree you calculated correctly, it might be a issue with micro stepping on the Z axis or disabling z axis when not in use. . Make sure the line #define DISABLE_Z is set to false in your configuration.h. If that does not work you can disable micro stepping by pulling the jumpers under the stepper driver(assuming you have RAMPS) and then run the calculator again. You should get 250, that helped to solve my Z height issues and I do not need the resolution that microstepping gave me. Printing at .1 .2 .3 etc is enough for my uses.

I've been working on this for a while now, the Z axis still is not moving correctly. without micro-stepping, prints are still coming out flatter than they should be. Any other ideas?

It seems to be a problem with layer height. I was trying to print at 200 micron thick layers, at 400 microns the prints seem to work better....

It sounds like you're missing steps, then. The easiest way to check is to get the printer to move up or down a specific distance and measuring how much it actually travelled.

If you find that you're missing steps, either increase the driver's vref or decrease the z axis speed.

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