Well, I can't say what's going on for sure. It seems like you've got it.
Double check your MIDI channel. I honestly don't have the time to play around with mine as I'm under a tight deadline to get another project done.
I will say this:
You'll of course have to make changes to the nanoKONTROL before you open up MyDMX, and don't forget to write the values. But, I think you know this and have done this, so I don't think that's the issue.
I'll see what I can do but don't expect miracles.
Here's some insight into my situation:
I have to FIGHT all day long to be able to work(starting as often as 5AM...), which can take until 10PM when the fight can stop(when the kids pass out from exhaustion and wife stops throwing attitude trips at me), and then I have from 10PM to 2AM to try to cram in all the work I was trying to accomplish the rest of the time. And by then, I'm too burned out to want to work.
Ah, the joys of being self employed.
But back to your situation:
I can't see why copying a scene would result in different or non-working results. There's no hardware layer sub-addressing going on, at least not to my knowledge and it's not within the MIDI spec. I know some devices use a device to device proprietary protocol for certain things(like cloning 2 Roland keyboards), but you have to throw at least one of them into that mode.