@Tom Speirs You are absolutly correct! the "Show Desktop" was stet to true, but for some reason in the versions 18.90 and upward, the Game Cube and Wii were not showing the RetroArch Emulator screen though it was present in the background. After doing some more investigation, i found that if I switched the RetroArch core from loading video = Vulkan to video = glcore, then everything worked again. It was just odd that the "Vulkan" video output worked for RetroArch for all console platforms before the update. Sorry for jumping the gun on this one! I deffenitly will be more intrusive in my investigations of emulators prior to posting next time. However, for those who do run into the same issue as I did, this is something they can check out in their RetroArch Emulator should it occur.
Thank you for the speedy response aswell! :)