Z axis is wrong direction ONLY during print

[niemanj]

I have a new Prusa clone that I just built and I cannot get it to print.

The z-axis jog direction is correct, the homing and bed probing works correctly, however as soon as it starts printing my printers moves down in Z for each layer. I cannot figure out why or how to fix it.

I have given the same g-code commands (G1 z0.20… G1 z0.40, etc.) to the printer manually and it moves in the correct direction, even though while it is printing it moves towards the bed for each layer. I tried inverting the z-axis however then everything moves the wrong direction.

Is there a reason the z-axis seems to flip once it starts printing? It would also mean that it is resetting the origin above the first layer and works down- which seems unlikely. I have attached an excerpt of my g-code from Slic3r for my custom clone machine. You will notice there is a 10mm z-offset which I used to confirm the fact it gets closer to the bed with each layer.

; generated by Slic3r Prusa Edition 1.41.0+win64 on 2018-11-10 at 15:41:53

; external perimeters extrusion width = 0.45mm
; perimeters extrusion width = 0.45mm
; infill extrusion width = 0.45mm
; solid infill extrusion width = 0.45mm
; top infill extrusion width = 0.40mm
; first layer extrusion width = 0.42mm

M201 X9000 Y9000 Z500 E10000 ; sets maximum accelerations, mm/sec^2
M203 X500 Y500 Z12 E120 ; sets maximum feedrates, mm/sec
M204 P2000 R1500 T2000 ; sets acceleration (P, T) and retract acceleration ®, mm/sec^2
M205 X10.00 Y10.00 Z0.20 E2.50 ; sets the jerk limits, mm/sec
M205 S0 T0 ; sets the minimum extruding and travel feed rate, mm/sec
M107
M115 U3.1.0 ; tell printer latest fw version
M83 ; extruder relative mode
M204 S2000 T1500 ; MK2 firmware only supports the old M204 format
M104 S230 ; set extruder temp
M140 S30 ; set bed temp
M190 S30 ; wait for bed temp
M109 S230 ; wait for extruder temp
M300 S3500 P300; Play Sound
G4 S2
G28 W ; home all without mesh bed level
;G29 mesh bed leveling
G1 Y-3.0 F1000.0 ; go outside print area
G92 E0.0
G1 X60.0 E9.0 F1000.0 ; intro line
M73 Q0 S38
M73 P0 R37
G1 X100.0 E12.5 F1000.0 ; intro line
G92 E0.0
M900 K45; Filament gcode
G21 ; set units to millimeters
G90 ; use absolute coordinates
M83 ; use relative distances for extrusion
;BEFORE_LAYER_CHANGE
G92 E0.0
;0.16

G1 E-0.80000 F2100.00000
G1 Z10.600 F10800.000
;AFTER_LAYER_CHANGE
;0.16
G1 X82.241 Y63.916
G1 Z10.160
G1 E0.80000 F2100.00000
M204 S1000
G1 F1200
G1 X82.764 Y63.054 E0.02584
G1 X83.200 Y62.645 E0.01536
G1 X83.710 Y62.331 E0.01536
G1 X84.273 Y62.126 E0.01536
G1 X84.865 Y62.039 E0.01536
G1 X105.004 Y62.036 E0.51665
G1 X105.550 Y62.087 E0.01406
G1 X106.076 Y62.238 E0.01406
G1 X106.563 Y62.481 E0.01395
G1 X107.000 Y62.812 E0.01406
G1 X107.368 Y63.217 E0.01406
G1 X107.656 Y63.684 E0.01406
G1 X107.853 Y64.195 E0.01406
G1 X107.952 Y64.734 E0.01406
G1 X107.963 Y85.094 E0.52232
G1 X107.759 Y86.084 E0.02595
G1 X107.236 Y86.946 E0.02584
G1 X106.783 Y87.368 E0.01590
G1 X106.247 Y87.689 E0.01601
G1 X105.657 Y87.891 E0.01601
G1 X105.037 Y87.964 E0.01601
G1 X84.902 Y87.963 E0.51654
G1 X83.916 Y87.759 E0.02584
G1 X83.054 Y87.236 E0.02584
G1 X82.632 Y86.783 E0.01590
G1 X82.311 Y86.247 E0.01601
G1 X82.109 Y85.657 E0.01601
G1 X82.036 Y85.037 E0.01601
G1 X82.037 Y64.902 E0.51654
G1 X82.229 Y63.974 E0.02431
G1 X82.602 Y64.051 F10800.000
G1 F1200
G1 X83.069 Y63.291 E0.02289
G1 X83.451 Y62.939 E0.01331
G1 X83.895 Y62.670 E0.01331
G1 X84.383 Y62.496 E0.01331
G1 X84.897 Y62.424 E0.01331
G1 X105.004 Y62.422 E0.51583
G1 X105.942 Y62.600 E0.02449
G1 X106.753 Y63.109 E0.02459
G1 X107.321 Y63.877 E0.02449
G1 X107.571 Y64.798 E0.02449
G1 X107.577 Y85.075 E0.52020
G1 X107.397 Y85.949 E0.02289
G1 X106.931 Y86.709 E0.02289
G1 X106.533 Y87.073 E0.01382
G1 X106.069 Y87.346 E0.01382
G1 X105.559 Y87.517 E0.01382
G1 X105.024 Y87.578 E0.01382
G1 X84.925 Y87.577 E0.51563
G1 X84.051 Y87.397 E0.02289
G1 X83.291 Y86.931 E0.02289
G1 X82.927 Y86.533 E0.01382
G1 X82.654 Y86.069 E0.01382
G1 X82.483 Y85.559 E0.01382
G1 X82.422 Y85.024 E0.01382
G1 X82.423 Y64.925 E0.51563
G1 X82.590 Y64.110 E0.02134
G1 F8640
G1 X83.069 Y63.291 E-0.21913
G1 X83.451 Y62.939 E-0.11979
G1 X83.895 Y62.670 E-0.11979
G1 X84.383 Y62.496 E-0.11979
G1 X84.897 Y62.424 E-0.11979
G1 X85.164 Y62.424 E-0.06169
G1 E-0.04000 F2100.00000
G1 Z10.760 F10800.000
G1 X84.077 Y63.011
G1 Z10.160
G1 E0.80000 F2100.00000
G1 F1200
G1 X84.929 Y62.808 E0.02247
G1 X105.004 Y62.807 E0.51502
G1 X105.804 Y62.960 E0.02090
G1 X106.496 Y63.397 E0.02099
G1 X106.980 Y64.057 E0.02099
G1 X107.188 Y64.848 E0.02099
G1 X107.192 Y85.055 E0.51839
G1 X107.037 Y85.811 E0.01979
G1 X106.628 Y86.469 E0.01989
G1 X105.900 Y87.000 E0.02311
G1 X105.017 Y87.193 E0.02320
G1 X84.941 Y87.192 E0.51502
G1 X84.186 Y87.036 E0.01979
G1 X83.531 Y86.628 E0.01979
G1 X83.000 Y85.900 E0.02311
G1 X82.807 Y85.017 E0.02320
G1 X82.808 Y64.941 E0.51502
G1 X82.964 Y64.186 E0.01979
G1 X83.372 Y63.531 E0.01979
G1 X84.028 Y63.047 E0.02093
; PURGING FINISHED
G1 F8640
G1 X84.929 Y62.808 E-0.21503
G1 X87.289 Y62.808 E-0.54497
G1 E-0.04000 F2100.00000
G1 Z10.760 F10800.000
G1 X85.596 Y80.147
G1 Z10.160
G1 E0.80000 F2100.00000
G1 F1200
G1 X85.596 Y65.596 E0.37330
G1 X104.404 Y65.596 E0.48253
G1 X104.404 Y84.404 E0.48253
G1 X85.596 Y84.404 E0.48253
G1 X85.596 Y80.207 E0.10769
G1 X85.210 Y80.207 F10800.000
G1 F1200
G1 X85.210 Y65.210 E0.38473
G1 X104.790 Y65.210 E0.50231
G1 X104.790 Y84.790 E0.50231
G1 X85.210 Y84.790 E0.50231
G1 X85.210 Y80.267 E0.11604
G1 X85.436 Y79.877 F10800.000
G1 F8640
G1 X85.210 Y76.975 E-0.76000
G1 E-0.04000 F2100.00000
G1 Z10.760 F10800.000
G1 X86.494 Y84.289
G1 Z10.160
G1 E0.80000 F2100.00000
G1 F1200
G1 X85.885 Y83.680 E0.02219
G1 X85.885 Y83.132 E0.01410
G1 X86.868 Y84.115 E0.03581
G1 X87.416 Y84.115 E0.01410
G1 X85.885 Y82.584 E0.05575
G1 X85.885 Y82.037 E0.01410
G1 X87.963 Y84.115 E0.07569
G1 X88.511 Y84.115 E0.01410
G1 X85.885 Y81.489 E0.09563
G1 X85.885 Y80.942 E0.01410
G1 X89.058 Y84.115 E0.11557
G1 X89.606 Y84.115 E0.01410
G1 X85.885 Y80.394 E0.13552
G1 X85.885 Y79.847 E0.01410
G1 X90.153 Y84.115 E0.15546
G1 X90.701 Y84.115 E0.01410
G1 X85.885 Y79.299 E0.17540
G1 X85.885 Y78.752 E0.01410
G1 X91.248 Y84.115 E0.19534
G1 X91.796 Y84.115 E0.01410
G1 X85.885 Y78.204 E0.21528
G1 X85.885 Y77.657 E0.01410
G1 X92.343 Y84.115 E0.23522
G1 X92.891 Y84.115 E0.01410
G1 X85.885 Y77.109 E0.25517
G1 X85.885 Y76.562 E0.01410
G1 X93.438 Y84.115 E0.27511
G1 X93.986 Y84.115 E0.01410
G1 X85.885 Y76.014 E0.29505
G1 X85.885 Y75.467 E0.01410
G1 X94.533 Y84.115 E0.31499
G1 X95.081 Y84.115 E0.01410
G1 X85.885 Y74.919 E0.33493
G1 X85.885 Y74.372 E0.01410
G1 X95.628 Y84.115 E0.35487
G1 X96.176 Y84.115 E0.01410
G1 X85.885 Y73.824 E0.37482
G1 X85.885 Y73.277 E0.01410
G1 X96.723 Y84.115 E0.39476
G1 X97.271 Y84.115 E0.01410
G1 X85.885 Y72.729 E0.41470
G1 X85.885 Y72.181 E0.01410
G1 X97.819 Y84.115 E0.43464
G1 X98.366 Y84.115 E0.01410
G1 X85.885 Y71.634 E0.45458
G1 X85.885 Y71.086 E0.01410
G1 X98.914 Y84.115 E0.47452
G1 X99.461 Y84.115 E0.01410
G1 X85.885 Y70.539 E0.49447
G1 X85.885 Y69.991 E0.01410
G1 X100.009 Y84.115 E0.51441
G1 X100.556 Y84.115 E0.01410
G1 X85.885 Y69.444 E0.53435
G1 X85.885 Y68.896 E0.01410
G1 X101.104 Y84.115 E0.55429
G1 X101.651 Y84.115 E0.01410
G1 X85.885 Y68.349 E0.57423
G1 X85.885 Y67.801 E0.01410
G1 X102.199 Y84.115 E0.59417
G1 X102.746 Y84.115 E0.01410
G1 X85.885 Y67.254 E0.61412
G1 X85.885 Y66.706 E0.01410
G1 X103.294 Y84.115 E0.63406
G1 X103.841 Y84.115 E0.01410
G1 X85.885 Y66.159 E0.65400
G1 X85.885 Y65.885 E0.00705
G1 X86.159 Y65.885 E0.00705
G1 X104.115 Y83.841 E0.65400
G1 X104.115 Y83.294 E0.01410
G1 X86.706 Y65.885 E0.63406
G1 X87.254 Y65.885 E0.01410
G1 X104.115 Y82.746 E0.61412
G1 X104.115 Y82.199 E0.01410
G1 X87.801 Y65.885 E0.59418
G1 X88.349 Y65.885 E0.01410
G1 X104.115 Y81.651 E0.57424
G1 X104.115 Y81.104 E0.01410
G1 X88.896 Y65.885 E0.55430
G1 X89.444 Y65.885 E0.01410
G1 X104.115 Y80.556 E0.53435
G1 X104.115 Y80.009 E0.01410
G1 X89.991 Y65.885 E0.51441
G1 X90.539 Y65.885 E0.01410
G1 X104.115 Y79.461 E0.49447
M73 Q2 S37
M73 P2 R36
G1 X104.115 Y78.914 E0.01410
G1 X91.086 Y65.885 E0.47453
G1 X91.634 Y65.885 E0.01410
G1 X104.115 Y78.366 E0.45459
G1 X104.115 Y77.819 E0.01410
G1 X92.181 Y65.885 E0.43465
G1 X92.729 Y65.885 E0.01410
G1 X104.115 Y77.271 E0.41470
G1 X104.115 Y76.724 E0.01410
G1 X93.276 Y65.885 E0.39476
G1 X93.824 Y65.885 E0.01410
G1 X104.115 Y76.176 E0.37482
G1 X104.115 Y75.629 E0.01410
G1 X94.371 Y65.885 E0.35488
G1 X94.919 Y65.885 E0.01410
G1 X104.115 Y75.081 E0.33494
G1 X104.115 Y74.533 E0.01410
G1 X95.467 Y65.885 E0.31499
G1 X96.014 Y65.885 E0.01410
G1 X104.115 Y73.986 E0.29505
G1 X104.115 Y73.438 E0.01410
G1 X96.562 Y65.885 E0.27511
G1 X97.109 Y65.885 E0.01410
G1 X104.115 Y72.891 E0.25517
G1 X104.115 Y72.343 E0.01410
G1 X97.657 Y65.885 E0.23523
G1 X98.204 Y65.885 E0.01410
G1 X104.115 Y71.796 E0.21529
G1 X104.115 Y71.248 E0.01410
G1 X98.752 Y65.885 E0.19534
G1 X99.299 Y65.885 E0.01410
G1 X104.115 Y70.701 E0.17540
G1 X104.115 Y70.153 E0.01410
G1 X99.847 Y65.885 E0.15546
G1 X100.394 Y65.885 E0.01410
G1 X104.115 Y69.606 E0.13552
G1 X104.115 Y69.058 E0.01410
G1 X100.942 Y65.885 E0.11558
G1 X101.489 Y65.885 E0.01410
G1 X104.115 Y68.511 E0.09564
G1 X104.115 Y67.963 E0.01410
G1 X102.037 Y65.885 E0.07569
G1 X102.584 Y65.885 E0.01410
G1 X104.115 Y67.416 E0.05575
G1 X104.115 Y66.868 E0.01410
G1 X103.132 Y65.885 E0.03581
G1 X103.679 Y65.885 E0.01410
G1 X104.289 Y66.494 E0.02219
;BEFORE_LAYER_CHANGE
G92 E0.0
;0.36

G1 F8640
G1 X103.679 Y65.885 E-0.19895
G1 X103.132 Y65.885 E-0.12643
G1 X104.115 Y66.868 E-0.32107
G1 X104.115 Y67.360 E-0.11356
G1 E-0.04000 F2100.00000
G1 Z10.760 F10800.000
;AFTER_LAYER_CHANGE
;0.36
M104 S240 ; set temperature
M140 S75 ; set bed temperature
; PURGING FINISHED
G1 X91.807 Y65.632
G1 Z10.360
G1 E0.80000 F2100.00000
M204 S800
…