Make sure you don't move you sticks while the controller is connecting, that could be your issue.
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Try re downloading the game. If re downloading doesn't work, you could try updating DirectX: https://www.microsoft.com/en-us/download/details.aspx?id=35
If that doesn't work, make sure you are using a dedicated graphics card to render the game, that might be a cause.(?)
Absolutely amazing ending. Although if you update this game with an extra boss, or maybe even create Yo Noid 3, or even if you don't make more content relating to this game, please make your next final boss take place in a level, I think it would add a very interesting twist on a boss fight!