@appleJimmies
Try it with a different microSD card. It sounds like the data is getting corrupted on shutdown. This usually happens with cheap generic microSD cards.
You might also try disabling Save Metadata On Exit in EmulationStation.
Check that your power adapter is 5V 2.5A.
Also, I doubt that you're doing this but I thought I would include it, if you're using some overclocking settings like especially overclocking your microSD card reader can cause weirdness like this.