OK i think i finally nailed down the issue. I think i need to start with a fresh USB drive. I changed the original recalbox directory to something different (i.e. recalbox-old) and allowed recalbox to set it up after a new install. I then just copied ROMS, Saves, BIOS, Cheats and the themes directories to the new recalbox directory. Doing it this way netted zero issues (although I had some issues with syncing my bluetooth controllers, but it eventually resolved itself after all updates and setting up was done.)
This seemed so trivial, especially since my entire experience with Linux involved 3 college credits 10 years ago. If this makes sense on why I had all of these issues, please accept my apologies for wasting your time.
Well, I fixed it. It looks like the default emulator was causing a problem. I swapped it to libreto gpsp and it started working. I thought that was the default but I guess not? Either way, it's working now so if anyone else has this issue, this is how I solved it.
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