I believe all the G-Code is correct, printing direct from Slic3r also works perfectly as does sending the G-Code to Octoprint. The problem seems to be only occur once the infill starts and might be related to acceleration or Repetier truncating something.
; generated by Slic3r 1.3.1-dev on 2018-06-23 at 08:49:11
; external perimeters extrusion width = 0.45mm (2.19mm
3/s)
; perimeters extrusion width = 0.45mm (3.76mm
3/s)
; infill extrusion width = 0.45mm (12.53mm
3/s)
; solid infill extrusion width = 0.45mm (12.53mm
3/s)
; top infill extrusion width = 0.40mm (1.38mm
3/s)
M107
M83 ; extruder relative mode
M104 S215 ; set extruder temp
M140 S60 ; set bed temp
M190 S60 ; wait for bed temp
M109 S215 ; wait for extruder temp
G28 W ; home all without mesh bed level
G29 ; bed leveling
G1 Y0 F1000.0 ; go outside print area
G92 E0.0
G1 X60.0 E9.0 F1000.0 ; intro line
G1 X100.0 E12.5 F1000.0 ; intro line
G92 E0.0
M221 S100{else}95{endif}
M900 K30
G21 ; set units to millimeters
G90 ; use absolute coordinates
M83 ; use relative distances for extrusion
;BEFORE_LAYER_CHANGE
;0.2
G1 E-2.00000 F2100.00000
G1 Z0.600 F9600.000
;AFTER_LAYER_CHANGE
;0.2
G1 X90.996 Y91.238 F9600.000
G1 Z0.200 F9600.000
G1 E2.00000 F2100.00000
M201 X1000 Y1000
M204 P1000 T1000
G1 F1800
G1 X91.557 Y90.696 E0.02447
G1 X91.961 Y90.345 E0.01676
...
G1 X91.263 Y91.504 F9600.000
G1 F1800
G1 X91.815 Y90.971 E0.02406
G1 X92.198 Y90.638 E0.01594
G1 X92.778 Y90.184 E0.02308
...
G1 X91.221 Y91.548 E0.01407
G1 F7680
G1 X91.483 Y91.284 E-0.09638
G1 F7680
G1 X91.483 Y91.284 E-0.00001
G1 F7680
G1 X91.505 Y91.262 E-0.00816
G1 F7680
G1 X91.564 Y91.205 E-0.02141
G1 F7680
G1 X91.587 Y91.184 E-0.00816
G1 F7680
G1 X91.587 Y91.183 E-0.00003
G1 F7680
G1 X91.815 Y90.971 E-0.08078
G1 F7680
G1 X91.876 Y90.916 E-0.02158
G1 F7680
G1 X92.111 Y90.712 E-0.08079
G1 F7680
...
I can share the complete G-Code, stl, Slic3r settings if it would be of any use ?