just replace the boot.dol in your apps/usbloader_gx/ folder with the new one.
@Gamefreakblog : that's really strange.
based on your screenshot on the previous page, it seems correctly setup.
Also, like said, you could see that the path is the correct one as it lists the game folders.
I don't think you have a hidden partition (USB flash drives usually don't have one), and even if it did your partition would be named "usb2:/" instead of 1 (1 being the first hidden partition).
I don't think the issue is the drive either, or else it will not mount, and you will not see the used/remaining size correctly.
Maybe there's an error in the "gamecube source" seting? but last time I tried it, it worked fine. you have "only MAIN path" selected, so it should look for games only on usb1:/games/, never look for SD:/games/
What you can try :
Dump a Gamecube game from inside USBLoaderGX (you will need a gamecube disc, obviously. just insert a disc, and the loader will ask if you want to install or mount it, choose install)
USBLoaderGX will dump the disc and put the full 1:1 ISO in the correct place, in the correct format, etc.
USBLoaderGX will then automatically list the new added game. this way, you can see on your drive where the game is stored, which folder name, filename, format etc.
If doing it THAT way the loader is still not seeing the new installed game, there's another error I don't understand yet. it may require more debugging.
Maybe your issue is not the settings or the drive, but your ISO are not real ISO.
maybe their format is wrong (a zip renamed to ISO, a corrupted dump, etc.)
Did you try your ISO on an emulator?