When you open the Slic3r gcode in MatterControl, do you immediatly just click "print" or do you try to slice it again? At what point does it add the leveling to the gcode?
I'm asking because I've tried what you're talking about but with Cura. I added the Pulse as a Prusa in Cura and saved the gcode for my model. Then I opened that gcode in mattercontrol and attempted to print. Unfortunately, when using the Cura gcode, MC would push the print head into the bed. I couldn't figure out how to get it to print level using gcode from another slicer.