So are you really asking if the decoder works differently when the loco is upside down?
By the way, it's often best practice to mount a decoder so there is some airflow around it, not enclosing it in a big tube of heat shrink or tape. Also, a big piece of tape across the bottom also can affect cooling.
Note, I say "best practice" since if you are running a low current motor (your Stainz), keeping the decoder cool is not usually a concern. Heavy loads, big motors, grades are where you want to give the decoder some room to breathe so to speak.
I think you are seeing operation unloaded/no resistance vs. running on a track, with drag on the wheels and drivetrain. I'm still in the out of quarter camp.
Greg