Try to rename the folder in sd/atmosphere/contents rename the contents folder to something else and reboot it could be an outdated homebrew or sys module or whatever. The funny thing is i had the same issue and it turned out to be reversnx the latest version uninstalling it fixed my blackscreen...
If you mean the games wont show on wiiflow you need to load wiiflow press home and press reload cache you need to do it to get new downloaded covers to show too.
Try the latest wiiflow lite and make sure you turn the global cios setting to auto and the game setting to auto. And your syscheck is perfect. I just tried city folk on the latest wiiflow lite with cios settings set to auto and it works for me have you tried usb loader gx...
That sucks im out of ideas maybe try updating to the latest version of wiiflow lite it will auto choose what cios to use for the right games and or try a different game dump https://github.com/Fledge68/WiiFlow_Lite/releases
You need cios 248 base 38 to play animal crossing city folk you can get the cios wads from modmii you might as well update all your cios to d2x v11. https://wiibrew.org/wiki/IOS38
I think i might of found a bug with r1281 if i go to gui settings and turn off show play count then the remember last game setting gets turned off so if i choose a game like mario kart and then switch to select loader mode and change it to emunand or gamecube titles then when i turn it back to...
Setting emunand channel path to full wont save to sd card its another setting i cant remember it and if you dump your emunand with usb loader gx then wiiware games wont work its broken dump your nand with bootmii and extract the nand.bin with showmiiwads and use the extracted nand it gives you...
I would check the drive for errors with your pc then load gx loader and choose reload sd its the sd card icon if that does not work then maybe yor hdd is failing.
Do you have those channels on the home menu if so then you have system channels checked if not then there on emunand on the top of the loader screen you can check and uncheck nand,emunand,gamecube,and wii games.
My dog used to chase off my neighbors cat from our yard, till one day the cat stood its ground, and paw slapped the shit out of my dog, now the cat wonders thru my yard, and my dog don't even care anymore, he's like f that cat. Lol