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Hi Phoclure,
I've just a quick look at your data. If you take the first 10mm as a base layer issue that throws the first and second 10mm off to a degree (eg, overextrusion on the base layer/first few solid layers which take a few layers for the print to build up and overcome) then the 3rd, 4th and 5th layers all look more consistent.
The difference between your 2nd to 5th levels varies from 9.65 to 9.8mm when you've asked for 10mm. Have you checked your z-axis steps per mm value? If this is off, then it would explain why when you ask for 10mm you only get 9.8mm. Check out the calculators are https://www.prusaprinters.org/calculator/#stepspermmlead to determine what your z-axis estep values should be.
Going off of your figures - It looks like your z-axis estep values are under by 2%. Not down your original z-axis estep number, then try multiplying it by 1.0204 and then try reprinting the piece.
Good luck!