Seems to be a common bug. Happens to me too and screws up my folder system. I only have 240 games total mostly NES, 10 Sega, 10 atari, 10 snes, and 3 n64. I got around it by not putting the n64 games on. Sigh. I feel like as many times as ive flashed my NES it's just not very happy anymore.