Question about USB loading my Roms

Alright, so I have homebrew on my Wii, and I've been playing Gamecube roms on Nintendont emulator and Gameboy Advance games on VisualBoyadvance GX.

They seem to load fine and I can save however once I've played the game once and I turn off the system if I go to play again the emulator either doesn't work or isn't displayed on homebrew (isn't reading it off the USB stick). I end up having to re-format the USB stick and reload my emulator and game(s) to play again.

Is there a reason for this? Its just because its kind of a pain in the @$$, but if theres no way to fix this I can deal with that.

Never heard anyone have this kind of issue before

I would check though the settings for both

I use both of those myself without issue though I do use real GC memcards rather than emulated with Nintendont

I also use a USB HDD rather than a stick that is known to have issues for some users mostly wii compat though not heard anything bad for GC or emulators