My roms are fine - I'm using the latest (0.2.97.36) FBA romset, which although newer than the set used by the retroarch core uses all the exact same roms as far as 'parent' roms are concerned (there may be additional clones and bootlegs in the newer set, but I avoid all but 'parent' roms for the sake of simplicity on the 3ds).
As for the 50mb limit; I believe it's a lot lower. I've found some roms with an uncompressed size of less than 40mb won't boot.
Well, nothing is saving in the config for me... regardless of it auto saving or manually saving, no changes are applied. I'll textedit it instead for the time being.