I turned it back on to reinstall everything so it is now in 7.2.2Reloaded.
When you reinstalled everything, how did you copy your files from the previous version?
Right is just copying ROMS/BIOS/Saves.
If you copied some configuration file together, this could be the problem, I recommend you try a reset to factory settings (available through the menu), you won't lose any personal files, but you will lose your custom settings.
I have to turn my rapsberry pi3 off and on again.
You can do this through Recalbox Manager, when really needed:
https://wiki.recalbox.com/en/tutorials/system/access/recalbox-manager-web-interface
except for N64
What emulator are you using?
Have you tried with another N64 emulator?