Without hands and eyes 'on', it's so difficult to diagnose at a distance.
The fact that it runs quietly and smoothly when upside down and no load 'suggests' to me a gear alignment problem rather than a motor problem, though it could be almost anything!
I am not familiar with the innards of this unit - what kind of gear train has it?
While it is running quietly, upside down, it could be helpful to place some load on the motor by gently holding a finger against a wheel to see if the noise returns under load. Also try gently moving the driven bogie(s?), vertically, radially and in a rocking motion. Somewhere among all the experimentation, you MIGHT find that the noise returns, together with an indication of what is creating it.
It could even be that the motor is just a little slack in its chassis mountings, so producing friction and/or bad gear mesh which is dependent on load and maybe on the positioning of the driven bogie.
Another helpful procedure, if it's not too difficult, would be to remove the motor altogether and see how it runs in isolation from the chassis, under no load and then with a small load applied by finger pressure on its shaft.
If you have another unit/loco that just happens to take the same motor, a motor swap could be revealing.
Although you say it appears to actually run OK and the noise is just an irritation, fact is that 'excessive' or untypical noise is indicative of friction/binding/wear/wasted power and will almost certainly lead to running problems later on - but you know this of course, which is why you are persisting with it!
Sorry this all looks a little bit vague on the page, but a good deal of careful experimentation and observation can sometimes take you to the root of a problem.
I'll be very interested to se how you get on.