@rumbaldo: Looking at your wiring everything seems to be ok. GND and VCC do not need to be swapped. To be sure, I have updated the ControlBlock article and added a diagram that shows the pin out with which I have successfully connected the original SNES controller front with the ControlBlock. You can find the diagram at https://www.petrockblock.com/2014/12/29/controlblock-power-switch-and-io-for-the-raspberry-pi/#Using_SNES_Controllers_with_the_ControlBlock.
Maybe you have a short somewhere?
Also it is important that only a single service uses the I2C port. Also, there were issues with overclocking. I have tested the bug fix as thoroughly as possible, but maybe there is still something wrong. You could try and set the overclocking setting back to “normal”. Also, you could check the functionality of the GPIO expanders by configuring the gamepad type as “arcade”, manually pulling each pin to GND and using the tool “jstest” to see the status changes of the virtual gamepads.