I had this problem and for some reason my es_systems.cfg file had lost some of the file extensions the emulators used. For example, it didn’t have in .smd under the Megadrive section meaning that although all my roms were still here, because they were .smd file extensions, it wasn’t picking them up. Adding this in worked fine.
I’ll add, I only had this problem when upgrading. If I did a clean 3.0 image it works without issues.