the problem with tuning on a box is there is no load on the engine. if there is no load the engine isnt working so when you drop it on the ground the tune is going to be too lean.
always tune on the ground. you CAN idle tanks off the ground, be sure to pre-heat and keep the engine 200F or higher, but for actual running purposes, do not tune with the wheels off the ground.
also make sure to bring the piston to Bottom dead center (piston as low as it can go in the sleeve) as soon as you can after turning it off. otherwise the sleeve will pinch the piston and it will get stuck and will cool down properly and get stretched out.