Yes, whenever I say upper or lower chain loop, I'm referring to them as they are with the bike upright. So the upper loop is still the upper loop even when it's on the bottom.

BTW- all this could have been avoided with a simple test that should be done before installing a new wheel.

Hold the wheel by the axle and spin it forward. Put your thumb against the cassette and you should only feel a trace of drag when it freewheels.

Some people simply spin the cassette and see how long it spins, but weight or inertia can affect that.

In any case, however you do it, check new wheels to confirm that the freewheel is truly free before installing.