Here is the log where I try all combinations. Also as I said, I can write to the MCU by flashing other firmware onto it. Klipper sends back "OK" when I enter a command. It is only Repetier-firmware which does not acknowledge commands, even after reinstall. Tried a few different versions of the firmware as well.
Offl:6:56:36.315: Ignored (offline):M360 ; get configuration
Offl:6:56:36.315: Ignored (offline):M539 S1
Exec:6:56:36.315: @getip
Offl:6:56:36.316: Ignored (offline):M117 192.168.1.144:3344
Mesg:6:56:37.436: Dtr: true Rts: true
Mesg:6:56:37.436: Connection started
Mesg:6:56:37.436: Printer reset requested - emergency:false
Mesg:6:56:37.436: Dtr: false Rts: false
Recv:6:56:38.055: Connection verified by:wait
Recv:6:56:38.056: wait
Send:6:56:38.056: N0 M110 N0
Recv:6:56:39.058: wait
Mesg:6:56:40.058: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:40.058: wait
Send:6:56:40.058: N1 M999 ; In case we did not reset recover from fatal state
Recv:6:56:41.057: wait
Mesg:6:56:42.060: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:42.060: wait
Send:6:56:42.060: N0 M110 N0
Recv:6:56:43.060: wait
Mesg:6:56:44.063: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:44.063: wait
Send:6:56:44.063: N1 M105 ; fetch first temperature
Recv:6:56:45.063: wait
Mesg:6:56:46.062: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:46.062: wait
Send:6:56:46.062: N2 M105
Recv:6:56:47.066: wait
Mesg:6:56:48.065: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:48.065: wait
Send:6:56:48.065: N3 M105
Recv:6:56:49.065: wait
Mesg:6:56:50.068: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:50.068: wait
Send:6:56:50.068: N4 M105
Recv:6:56:51.067: wait
Mesg:6:56:52.071: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:52.071: wait
Send:6:56:52.071: N5 M105
Recv:6:56:53.070: wait
Mesg:6:56:54.070: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:54.070: wait
Send:6:56:54.070: N6 M105
Recv:6:56:55.073: wait
Mesg:6:56:56.073: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:56.073: wait
Send:6:56:56.073: N7 M105
Recv:6:56:57.076: wait
Mesg:6:56:58.076: Warning: Seems like we missed a ok - continue sending.
Recv:6:56:58.076: wait
Send:6:56:58.076: N8 M105
Recv:6:56:59.075: wait
Mesg:6:57:00.079: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:00.079: wait
Send:6:57:00.079: N9 M105
Recv:6:57:01.078: wait
Mesg:6:57:02.081: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:02.082: wait
Send:6:57:02.082: N10 M105
Recv:6:57:03.081: wait
Mesg:6:57:04.080: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:04.080: wait
Send:6:57:04.080: N11 M105
Recv:6:57:05.084: wait
Mesg:6:57:06.083: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:06.083: wait
Send:6:57:06.083: N12 M105
Recv:6:57:07.083: wait
Mesg:6:57:08.086: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:08.086: wait
Send:6:57:08.086: N13 M105
Recv:6:57:09.086: wait
Mesg:6:57:10.089: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:10.089: wait
Send:6:57:10.089: N14 M105
Recv:6:57:11.089: wait
Mesg:6:57:12.088: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:12.088: wait
Send:6:57:12.088: N15 M105
Recv:6:57:13.092: wait
Mesg:6:57:14.091: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:14.091: wait
Send:6:57:14.091: N16 M105
Recv:6:57:15.094: wait
Mesg:6:57:16.094: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:16.094: wait
Send:6:57:16.094: N17 M105
Recv:6:57:17.093: wait
Mesg:6:57:18.097: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:18.097: wait
Send:6:57:18.097: N18 M105
Recv:6:57:19.096: wait
Mesg:6:57:20.096: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:20.096: wait
Send:6:57:20.096: N19 M105
Recv:6:57:21.099: wait
Mesg:6:57:22.099: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:22.099: wait
Send:6:57:22.099: N20 M105
Recv:6:57:23.102: wait
Mesg:6:57:24.101: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:24.102: wait
Send:6:57:24.102: N21 M105
Recv:6:57:25.101: wait
Mesg:6:57:26.104: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:26.104: wait
Send:6:57:26.105: N22 M105
Recv:6:57:27.104: wait
Mesg:6:57:28.107: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:28.107: wait
Send:6:57:28.107: N23 M105
Recv:6:57:29.107: wait
Mesg:6:57:30.106: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:30.106: wait
Send:6:57:30.106: N24 M105
Recv:6:57:31.110: wait
Offl:6:57:31.204: Ignored (offline):M105
Offl:6:57:31.204: Ignored (offline):M115 ; Check firmware and capabilities
Offl:6:57:31.204: Ignored (offline):M220 S100 ; set speed multiplier
Offl:6:57:31.204: Ignored (offline):M221 S100 ; set flow multiplier
Offl:6:57:31.204: Ignored (offline):M355 ; get light status
Offl:6:57:31.204: Ignored (offline):G92 E0 ; reset extruder position
Offl:6:57:31.204: Ignored (offline):G90 ; absolute coordinates
Offl:6:57:31.204: Ignored (offline):M82 ; absolute E values
Offl:6:57:31.204: Ignored (offline):G21 ; units are mm
Offl:6:57:31.204: Ignored (offline):M114 ; check position
Offl:6:57:31.204: Ignored (offline):M111 S6 ; debug flags
Offl:6:57:31.204: Ignored (offline):M360 ; get configuration
Offl:6:57:31.204: Ignored (offline):M539 S1
Exec:6:57:31.204: @getip
Offl:6:57:31.206: Ignored (offline):M117 192.168.1.144:3344
Mesg:6:57:32.327: Dtr: false Rts: false
Mesg:6:57:32.328: Connection started
Mesg:6:57:32.328: Printer reset requested - emergency:false
Mesg:6:57:32.328: Dtr: true Rts: true
Recv:6:57:32.748: Connection verified by:start
Recv:6:57:32.749: Printer reset detected:start
Recv:6:57:32.750: start
Send:6:57:32.750: N0 M110 N0
Recv:6:57:32.753: Info:PowerUp
Recv:6:57:32.753: Detected EEPROM version:20
Recv:6:57:32.757: Info:Autoleveling enabled
Recv:6:57:32.765: Transformation matrix: 0.999993 0.000000 0.003764 0.000008 0.999998 -0.002148 -0.003764 0.002148 0.999991
Recv:6:57:32.769: zDistortionCorrection:1
Recv:6:57:32.769: Free RAM:84360
Recv:6:57:32.770: SD init fail
Recv:6:57:32.773: SelectExtruder:0
Recv:6:57:32.773: FlowMultiply:100
Recv:6:57:33.555: wait
Mesg:6:57:34.554: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:34.554: wait
Send:6:57:34.555: N1 M999 ; In case we did not reset recover from fatal state
Recv:6:57:35.558: wait
Mesg:6:57:36.557: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:36.557: wait
Send:6:57:36.557: N0 M110 N0
Recv:6:57:37.561: wait
Mesg:6:57:38.560: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:38.560: wait
Send:6:57:38.560: N1 M105 ; fetch first temperature
Recv:6:57:39.560: wait
Mesg:6:57:40.563: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:40.563: wait
Send:6:57:40.563: N2 M105
Recv:6:57:41.563: wait
Mesg:6:57:42.562: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:42.562: wait
Send:6:57:42.562: N3 M105
Offl:6:57:43.004: Ignored (offline):M105
Offl:6:57:43.004: Ignored (offline):M115 ; Check firmware and capabilities
Offl:6:57:43.004: Ignored (offline):M220 S100 ; set speed multiplier
Offl:6:57:43.004: Ignored (offline):M221 S100 ; set flow multiplier
Offl:6:57:43.004: Ignored (offline):M355 ; get light status
Offl:6:57:43.004: Ignored (offline):G92 E0 ; reset extruder position
Offl:6:57:43.004: Ignored (offline):G90 ; absolute coordinates
Offl:6:57:43.004: Ignored (offline):M82 ; absolute E values
Offl:6:57:43.004: Ignored (offline):G21 ; units are mm
Offl:6:57:43.004: Ignored (offline):M114 ; check position
Offl:6:57:43.005: Ignored (offline):M111 S6 ; debug flags
Offl:6:57:43.005: Ignored (offline):M360 ; get configuration
Offl:6:57:43.005: Ignored (offline):M539 S1
Exec:6:57:43.005: @getip
Offl:6:57:43.006: Ignored (offline):M117 192.168.1.144:3344
Mesg:6:57:44.124: Dtr: true Rts: true
Mesg:6:57:44.125: Connection started
Mesg:6:57:44.125: Printer reset requested - emergency:false
Mesg:6:57:44.125: Dtr: true Rts: false
Recv:6:57:44.565: Connection verified by:wait
Recv:6:57:44.566: wait
Send:6:57:44.566: N0 M110 N0
Recv:6:57:45.568: wait
Mesg:6:57:46.568: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:46.568: wait
Send:6:57:46.568: N1 M999 ; In case we did not reset recover from fatal state
Recv:6:57:47.567: wait
Mesg:6:57:48.571: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:48.571: wait
Send:6:57:48.571: N0 M110 N0
Recv:6:57:49.570: wait
Mesg:6:57:50.574: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:50.574: wait
Send:6:57:50.574: N1 M105 ; fetch first temperature
Recv:6:57:51.573: wait
Mesg:6:57:52.573: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:52.573: wait
Send:6:57:52.573: N2 M105
Recv:6:57:53.576: wait
Mesg:6:57:54.576: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:54.576: wait
Send:6:57:54.576: N3 M105
Recv:6:57:55.575: wait
Mesg:6:57:56.578: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:56.579: wait
Send:6:57:56.579: N4 M105
Recv:6:57:57.578: wait
Mesg:6:57:58.581: Warning: Seems like we missed a ok - continue sending.
Recv:6:57:58.581: wait
Send:6:57:58.582: N5 M105
Recv:6:57:59.581: wait
Mesg:6:58:00.580: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:00.580: wait
Send:6:58:00.580: N6 M105
Recv:6:58:01.584: wait
Mesg:6:58:02.583: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:02.583: wait
Send:6:58:02.583: N7 M105
Recv:6:58:03.587: wait
Mesg:6:58:04.586: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:04.586: wait
Send:6:58:04.586: N8 M105
Recv:6:58:05.586: wait
Mesg:6:58:06.589: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:06.589: wait
Send:6:58:06.589: N9 M105
Recv:6:58:07.588: wait
Mesg:6:58:08.592: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:08.592: wait
Send:6:58:08.592: N10 M105
Recv:6:58:09.591: wait
Mesg:6:58:10.591: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:10.591: wait
Send:6:58:10.591: N11 M105
Recv:6:58:11.594: wait
Mesg:6:58:12.594: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:12.594: wait
Send:6:58:12.594: N12 M105
Recv:6:58:13.593: wait
Mesg:6:58:14.597: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:14.597: wait
Send:6:58:14.597: N13 M105
Recv:6:58:15.596: wait
Mesg:6:58:16.600: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:16.600: wait
Send:6:58:16.600: N14 M105
Recv:6:58:17.599: wait
Mesg:6:58:18.598: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:18.598: wait
Send:6:58:18.598: N15 M105
Recv:6:58:19.602: wait
Offl:6:58:20.045: Ignored (offline):M105
Offl:6:58:20.045: Ignored (offline):M115 ; Check firmware and capabilities
Offl:6:58:20.045: Ignored (offline):M220 S100 ; set speed multiplier
Offl:6:58:20.045: Ignored (offline):M221 S100 ; set flow multiplier
Offl:6:58:20.045: Ignored (offline):M355 ; get light status
Offl:6:58:20.045: Ignored (offline):G92 E0 ; reset extruder position
Offl:6:58:20.045: Ignored (offline):G90 ; absolute coordinates
Offl:6:58:20.045: Ignored (offline):M82 ; absolute E values
Offl:6:58:20.045: Ignored (offline):G21 ; units are mm
Offl:6:58:20.045: Ignored (offline):M114 ; check position
Offl:6:58:20.045: Ignored (offline):M111 S6 ; debug flags
Offl:6:58:20.045: Ignored (offline):M360 ; get configuration
Offl:6:58:20.045: Ignored (offline):M539 S1
Exec:6:58:20.045: @getip
Offl:6:58:20.046: Ignored (offline):M117 192.168.1.144:3344
Mesg:6:58:21.166: Dtr: true Rts: false
Mesg:6:58:21.166: Connection started
Mesg:6:58:21.166: Printer reset requested - emergency:false
Mesg:6:58:21.166: Dtr: false Rts: true
Recv:6:58:21.605: Connection verified by:wait
Recv:6:58:21.606: wait
Send:6:58:21.606: N0 M110 N0
Recv:6:58:22.604: wait
Mesg:6:58:23.604: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:23.604: wait
Send:6:58:23.604: N1 M999 ; In case we did not reset recover from fatal state
Recv:6:58:24.607: wait
Mesg:6:58:25.607: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:25.607: wait
Send:6:58:25.607: N0 M110 N0
Recv:6:58:26.606: wait
Mesg:6:58:27.610: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:27.610: wait
Send:6:58:27.610: N1 M105 ; fetch first temperature
Recv:6:58:28.609: wait
Mesg:6:58:29.612: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:29.613: wait
Send:6:58:29.613: N2 M105
Recv:6:58:30.612: wait
Mesg:6:58:31.611: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:31.611: wait
Send:6:58:31.611: N3 M105
Recv:6:58:32.615: wait
Mesg:6:58:33.614: Warning: Seems like we missed a ok - continue sending.
Recv:6:58:33.614: wait
Send:6:58:33.614: N4 M105