I think this is a common problem in Windows when you have multiple identical MIDI devices (e.g. 2 or 3 identical keyboards). Windows distinguishes them by just adding a number and as you have discovered it doesn't always assign the same number to the same device. The only sure way I can think of to get around it would be if you have the ability to change the actual device name within the MIDI device. i.e. if you can get at the device software and change "Moco for Lufa" to "Moco for Lufa A" in one of them and "Moco for Lufa B" in the next etc.
A less certain way would be to always power each device up in the same order and power them down in the reverse order but Windows will probably find a way to screw that up too.
Pete