Had the same problem and fixed it by deleting gamelist.xml and creating it again.

But one thing I noticed is a warning that comes when restarting ES:

/etc/init.d/S31emulationstation stop /etc/init.d/S31emulationstation start lvl0: System "favorites" is missing name, path, extension, or command!

Maybe that might help finding out why it happened.

@Bradley-Cable I had the same problem, I was using berryboot to boot the system, I installed the direct recalbox on the SD and it worked, if you are using berryboot or another system for multi-boot, try installing directly on the sd card