The GameCube iso present on the disc has nothing do to with the mounting problem.
it would first need to mount the HDD to see that there is a Gamecube iso on it.
Try connecting the HDD when you see the countdown, not before launching the loader (sometime it helps)
Is your HDD working with other loaders?
With other homebrew? Emulators, (like Snes9x GX) or mediaplayer (WiiMC)
That same HDD worked fine when formated in NTFS, but now doesn't work when formated in FAT32? Do you have multiple Partition?
Do you have a /wbfs/ folder in one of the partitions? (shouldn't be needed, but create one manually to test)
Could it be your partition information which is not correct? Try another HDD if you can, or use another partitioner to make a proper partition, re-format it to FAT32 (not FATex, it's not the same thing).