Bruce, Thanks for the reply. I don't have the old computer hooked up anymore, and I don't know if the specific physical USB ports are part of the problem. I don't know which physical port each of the three devices was plugged into. The three MIDI devices are exactly the same, so only the order might have changed.
I tried uninstalling the NanoKontrol and re-installing it to see if it would move to the end of the list, but it doesn't.
I thought I could get the order right by using the Move Checked Devices to Top button in the Setup / Midi Devices dialog.
However, that seems to be broken for the MIDI input. I'll submit a support request on that.