Spooky, I've just encountered the same problem, only my roms have the prefix CE in front of them. Everything was fine, all listed and working ok until i decided to delete some roms (about 60) and refresh the gamelist. This was in my cab so i repeated the same thing on my main computer and this didn't happen, luckily i could just copy the games&snap lists across to my cab.
btw This was using the Magic Engine emulator.