To play Gamecube games, you need DIOS MIOS, and a FAT32 partition on your hard drive. Importantly, the FAT32 partition needs to be the first partition on the drive, and active. You can check/do this by using a program like
EaseUS. Whilst you're there, I'd recommend backing up all your Wii images to your computer, and totally format the hard drive - WBFS is an outdated file system. Wii games can be loaded off FAT32 and NTFS, so you can just put all your Wii and Gamecube games on one partition.
If you decide to keep them separate, you need to make sure you go in to settings/config on your USB loader every time, and change the partition to WBFS (or NTFS) to FAT32. This is why your Gamecube games aren't showing. You'll then need to change back whenever you want to see your Wii games.