Quick question:
Can acceleration affect the printed objects size?
I fiddled around with a ripple-test-cube and adjusted the acceleration and jerk settings.
When I set acceleration to Marlins defaults (acceleration 3000 instead of 1500 before, max feedrate 500 instead of 300 before), the cube became 22mm tall instead of 20mm
While being on topic:
What are your used values for feedrate, acceleration and jerk for a prusa style printer?
Changing acceleration shouldn’t change Z height of the finished print, that’s bonkers.
@Ryan_Carlyle in theory, that’s correct. In reality, it did 
That should be because the printer doesn’t compensate the thicker layers resulting of increasing the feedrate and the acceleration. For instance lowering the first layer thickness in S3D to 90% has an effect on the z axis to just 0.18 every step (at least on CraftBot).
Try to raise the feedrate the same amount as the acceleration and your print should come out fine (at least theoretically)
@Daniel_Stauffer thanks for your answer! Up to now, I dont fully understand every setting. But as far as I know, speed settings (feed rate, acceleration, jerk) shouldnt habe something to do with the size? I didnt change any step settings
@Daniel_Stauffer that doesn’t make any sense. Both the slicer and firmware understand how to synchronize extruder flow rate to motion, and they all have since like 2009 when we switched from rpm based extruders to 5D firmware.
@Paul_Arnold open up your gcode file in a text editor and check the commanded height of the last layer versus the actual measured height of the print. If they’re different, it’s a firmware or hardware issue. For example Z steps/mm setting could be wrong or your Z axis could be skipping steps. (Actually that second one wouldn’t make sense with an i3 type printer since Z lifts, not lowers.)
A photo of your print and printer would help us diagnose.
@Ryan_Carlyle I’ll check that and post a pic tomorrow