Ok, so just to make sure I wasn't missing anything, I did the following...
Re-download and install RetroPie.
Connect to WiFi and install updates.
Download and install ControlBlock driver from RetroPie setup.
Configured new controllers on startup.
After doing some more testing, I discovered that my conltrol settings responded the same for NES, SNES, and all lr-* arcade emulators. Anything using mame4all seems to be governed by different setting. So for the moment, I'll stick with libretro emulators.
Now, when I go in to RetroArch from the RetroPie setup menu and make changes to the button configurations, a few things happen. Setting buttons for Restart and Quit RetroArch requires that I set a button for Toggle Hotkeys. I'd prefer not to have to do that. Making those button changes also causes Select+Start in NES and SNES to stop quiting RetroArch.
I feel like I'm getting closer, but the hotkeys are still throwing me off.
Any thoughts? Thanks.