Does it make sense that I would lose all my "custom" commands from the Quick Access Toolbar simply because I changed my Windows Desktop Theme? Because that's what seems to have happened.
"Custom" commands meaning those which I dragged/copied from the ribbon to dock there.
I don't have a solution for you, but I changed my Windows theme a couple of times and when I'd open my Civil 3D my quick access bar was fine. I have lots of customizations on it so I was concerned. I'm using Windows 7 Professional. Was the theme downloaded from MS or a third party site? It seems odd since it's the .cui file that saves those customizations.
The original theme was one that came with the computer. I switched to a plain standard MS theme.
There were only 10 or so that I had to replace, so it wasn't a huge deal. It just seemed odd, that's all.