I have the exact same problem.
IOS58 is installed and I have no problems loading games from USB with FCE Ultra GX 3.2.3, Snes9x GX 4.2.5 or VBA GX 2.2.2.
Homebrew Channel 1.0.8 also loads everything just fine from USB using IOS58.
I have tried deleting SD:\genplus and removed SD card in the...