Emulationstation is just a front-end, it doesn't run games - it merely starts the configured emulator with some arguments. If you're looking to start RetroArch right away with your ROM, then replace the %ROM_RAW% with the full path to the ROM file.
I'd say your card or filesystem on the card is corrupted. If flashing the RetroPie image on the card doesn't solve this problems, you should get another card.