So,
I started the printer, (standalone) not connected to the Pi. I rebooted the Pi with Repetier Server running, then I connected the printer and the Pi.
Then I pressed "Home all" on the touchscreen with Repetier running:
12:28:56.028: N11 G28
12:29:35.466: echo:busy: processing (19)
12:29:35.509: X:160.00 Y:114.50 Z:12.20 E:0.00 Count X:12800 Y:9160 Z:4880 // LCD says 160 / 115 / 12.2
12:29:35.509: ok
Then I pressed "move up" with "1" selected:
12:30:15.673: N12 G1 Z1.00 F720 - the extruder moves DOWN from z=12.2 to z=1
12:30:15.680: ok
I pressed the same "Move up" button again.
12:30:26.672: N13 G1 Z2.00 F720 - extruder moves up by "1" - LCd shows z=2
12:30:26.674: ok
12:30:28.261: N14 G1 Z3.00 F720 - again, moves up by 1 and z=3 on the LCD
12:30:28.266: ok
So the first command let#s it move to z=1, but then it adds up incrementally.
The same sequence shows a correct behaviour on the Prusa mk3 <-- CORRECTION: The nozzle is so low on the Prusa aftert homing, it actually has to move up as it moves to z=0 on the Prusa during homing.