In general, I’ve never tried to compile Marlin with anything newer than 1.0.x Arduino IDE. Arduino 1.6.x contains changes even over the 1.5.x IDE that may require settings changes. I always target Mega 2560.
From what you posted though, it doesn’t seem like your Marlin version is what is making it lift twice. It seems like the Kudo3D controller software is sending the lift sequence command twice.