What version are you using?
For me it stays the same because in command line
09:52:56.441 : Slic3r command:C:\Users\littwin\Documents\Projekte\Repetier-Host\src\RepetierHost\bin\Debug\Slic3r\slic3r-console.exe --load "slic3r_settings.ini" --dont-arrange -o "composition.gcode" "composition.amf"
The --dont-arrange tells slic3r to not move position. Check if you have that also when calling it. With default settings under windows this is the case, but in older version (selectable in slicer manager) this might be missing because the option did not exist.