I suggest using a HDD instead, flash drives cause no end of trouble with USB loaders.
Did you have Loader IOS set to IOS58 in USB Loader GX by any chance? That might explain why it showed the games before, but won't show them after resetting the settings. Loader IOS as IOS58 helps sometimes, but usually the games still won't load.
Edit: Also note that with self powered hard drives you need an Y-cable or a powered hub for extra power since the Wii U doesn't provide enough through a single port.
I have a question about Medicat if anyone can answer.. My windows install is corrupt and wont boot. Does Medicat allow you to run DISM online or do an inlace upgrade? Trying to do some sort of repair install or recovery without a fresh installation