Did you find a solution to this madadivad? I'm having the same issue with my Lulzbot - they have their own branch of Cura, but the plugin is likely identical. Looking at the gcode, I saw that right before it starts printing after the pause there's M82 (set extruder to absolute) and G92 E## (which sets the extruder to a certain position). My guess is that when I'm manually extruding during the pause to load the new filament, the print job is actually seeing that as the extruder moving forward. Then when it gets to that G92 command it assumes it has to retract a bunch to get to that position. Only thing is I don't see any options to switch to relative mode in Cura as smartavionics has suggested. Perhaps the standard version of Cura has it, but Lulzbot removed it from their's?