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Wiring the controlBlock to the system controller ports actually was a concern of mine from the beginning, for this exact reason. The SNES controller port photo diagram on the site led me to believe that it would not be an issue, but with the SNES mini, it actually is an issue.
After another (seemingly) failed attempt at the driver installation, I began to hack the board and made cuts to separate the system controller ports from the SNES main board thinking that this would sever the traces to the SNES IC’s. Unfortunately this did not help.
I then separated the system controller ports completely from the SNES man in board by cutting the pins from the board and soldering directly to the pins. This isolated the controller ports from the SNES system case and main board board, and indeed cured the issue of all switches being activated at once and not allowing configuration or use of the controllers via the ControlBlock.
The construction on the SNES Mini differs in that the controller port is part of the main board, the pins that connect with the controller cables are soldered directly to the main board, there are no ribbons or wires that can be disconnected to isolate the controller ports.
With this discovery, it should be noted in the ControlBlock installation instructions that: if a second generation SNES (SNES Mini) is the system being used to connect directly to, the controller ports need to be “completely” separated from the SNES board. Controller wires from the ControlBlock must be connected to an SNES mini controller port that is isolated from the SNES main board.
My retropie SNES Mini system is fully operational now! Below is a photo of the SNES mini controller port isolated from the SNES main board. I will also post a few photos of the finished working system.
Thank you for all of your help!