Did you have an EFI (or some other kind of reserved) partition on the drive to begin with? If not, then cleaning the drive in diskpart probably wouldn't have mattered.
The only reason I had to do so was because the 200MB EFI partition was preventing WBFS Manager from formatting the drive.
Your problem may have a completely unrelated cause. I hope you're able to figure it out.
On a slightly unrelated note, I was initially unable to get the installed Wii games on my hard drive to appear in USB loader GX via homebrew channel. If anybody else has the same problem, I restarted it, then tried again, but through the frontloader (which makes a 'shortcut' channel on the main Wii menu) instead of through the homebrew channel, and the list was instantly populated with the games on the HDD, and it now finds them even if I go to the loader through the homebrew channel. I also had to set the global video mode in USB loader GX to "disc default" as it was giving me a black screen whenever I started a game that didn't match my Wii's region.
The only reason I had to do so was because the 200MB EFI partition was preventing WBFS Manager from formatting the drive.
Your problem may have a completely unrelated cause. I hope you're able to figure it out.
On a slightly unrelated note, I was initially unable to get the installed Wii games on my hard drive to appear in USB loader GX via homebrew channel. If anybody else has the same problem, I restarted it, then tried again, but through the frontloader (which makes a 'shortcut' channel on the main Wii menu) instead of through the homebrew channel, and the list was instantly populated with the games on the HDD, and it now finds them even if I go to the loader through the homebrew channel. I also had to set the global video mode in USB loader GX to "disc default" as it was giving me a black screen whenever I started a game that didn't match my Wii's region.