I just had this issue on the same build and same hardware.
All I did was click the green full screen button at the top left of the Citra window and the game appeared.
You can click it again to make Citra go back in to windowed mode and it'll stay normal.
Sorry for the slight necro, Hope this...
yo guys the sonic x shadow generations trailer dropped today, and shadow just straight up decided, and i hate (love) to bring this dead meme up, but, it's morbin time