So I finally got the issue resolved with getting my Key Commands to work with my X-tra Keys unit (Details for that story here: https://www.steinberg.net/forum/viewtopic.php?f=177&t=36438 ). I programmed in the commands from scratch, as I was never able to import any of the presets I’d saved from earlier iterations. Just when I think I’m in business, ALL OF THE KEY COMMANDS (from the QWERTY or the X-keys) stopped working! 
I closed the project an re-opened it, no change. I had to completely shut down N6 and re-open it to get the link back. This has now happened 3 times and, needless to say it’s gotten really annoying. So I statrted researching to see if anyone else was having this problem. Sure enough, I found this thread https://www.steinberg.net/forum/viewtopic.php?f=175&t=36665 on the Cubase Forum. The User described the same problem and fix exactly as I experienced it.
Have I come across some kind of bug here? Anyone else on the Nuendo side having this issue with N6?