When paused, Simplify3D remembers all the manual motor commands you send and reverses them on Resume in order to get the print head back in the position it was in when you paused. All good.
It also seems to do that with the extruder motor, leading to blobs of "purposely" extruded plastic or no-filament gaps when Simplify3D returns the extruder motor to the "zero-change position." This makes filament changes during printing problematic, forcing the user to keep track of all the extruder commands sent during pause.
Please remove the extruder motor from the "resume after pause" commands tracking or allow the user to turn that "feature" off.
Robert