I found this when looking for the reason my Record Enable buttons no longer responded to the Up/Down arrow keys. Here is the post I wrote in the Troubleshooting Forum:
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Yes, the Commands Window was still set for the up/down Record enable, but MOTU has added "Nudge Up" and "Nudge Down" commands, as well as "Nudge" commands for the Custom Console Window, and they assigned the up/down arrows to all of them!
That's all well and good, but I'm going to have to find a new set of commands for either the Record-Enable or the nudge commands; they can't share the same arrow keys.
So, if you have this problem, the answer is to reassign some commands in the Commands Window which are assigned the same keys. Specifically, these are:
Track
- Record Enable Next Track
Record Enable Previous Track
- Nudge UP
Nudge DOWN
- Nudge UP
Nudge DOWN

See all those transposed tracks? Those were altered while I was attempting to change the record-enabled track. Furthermore, any time you happen to hit the arrows by accident or for any other reason, you will have just transposed a note, selection, or whole track or group of tracks by a half-step for each time you struck the key.
It is essential that you change the command from arrow keys to something that can only be hit deliberately.
Shooshie