The FAT32 partition MUST be the first partition on the drive or Nintendont will fail to find it. The WBFS file system is ancient and you are better off using FAT32 and a Wii Backup tool that will split the >4GB isos for you.
I did a only fat32 (primary, 64KB cluster) patition for wbfs games and gamecube but still not recognizing gamecube games... when I use this on homebrew channel don't work too.