You either :
- Don't have latest version of USBLoaderGX. Verify in settings>Credit.
if you see "3.0c" you have the channel version, it's outdated and support is dropped. please, delete the channel and reinstall the Forwarder channel instead to load the loader from SD card.
If USBLoaderGX is updated correctly, you should see "r1256" on the boot screen sequence.
- You didn't tell the loader that you want to use nintendont.
There are 3 methods to launch gamecube games, it's not hard for the devs, it's up to the users to select the launching method.
By default, it's set to launch gamecube DISCs, the default behavior of the console and the method used by the first backup loader : DIOS MIOS and DIOS MIOS Lite.
Then, there's Devolution
And finally there's Nintendont.
You have to tell the loader if you want to use MIOS (default), Devolution or Nintendont
Settings>Loader settings>Gamecube mode
To me, it looks like your issue is the first one.
3.0 didn't support USB, because at release time NO backup loader supported USB, only DML (for SD) was released.
After each gamecube backup loader release, I updated the loader to support them and all their features, being USB or all their settings.
You have to use the homebrew+forwarder channel.
The full channel is not used anymore (both dangerous and not compatible with WiiU)