Are you booting Atmosphere via Fusee or Hekate? If you are booting via Hekate and they aren't working, those games most likely need the ACID patch which Hekate doesn't support so you will have to either use ReiNX or boot Atmosphere via Fusee. If you are booting via Fusee, the patches on SDSetup are for booting via Hekate not Fusee. For booting via Fusee, you need
these patches. If you are still experiencing issues, your SD card may be corrupted if you are using exFAT in which case I highly recommend reformatting the SD card to FAT32 which also means you'll have to reinstall all of your corrupted games. If you don't want to reformat, try another CFW like ReiNX to see if the issue persists.