Hello,
It's a thread from 2013, but it's fine as it's still related to your issue.
like said, some games are not working with USBLoaderGX current way of handling emuNAND.
I don't know which games you tried to run, but most N64 VC channel will not work. Users often start testing emuNAND with those games, and it doesn't work, so we don't know if the game or the setup is wrong.
I recommend Cave story or La Mulana for a first test. I know these games are working fine.
We started a compatibility list here :
http://wiki.gbatemp.net/wiki/Wii_EmuNAND_Channel_Compatibility_List
Be sure to try a working game based on the current cIOS you are using.
Try to put your EmuNAND path to SD.
sometime, USB doesn't work with old cIOS. (it's an issue in USBLoaderGX, I didn't find how to fix it)