Do you all use uStealth to get a second HDD working for wii games? I was encountering this exact problem ever since I started using uStealth, and it showed up specifically after I wup installed a wii u game with a ustealth drive still connected. Even after I stopped using that uStealth drive the problem still persisted.
Fast forward to now, I've just setup all of my homebrew on another wii u without ever touching ustealth, and gamecube injects work perfectly fine. No blackscreens, boots normally 100% of the time.