Hi Els,
From the Bpod Console, click the settings (wrench) icon, and select 'ports'. There, you should find a checkbox for each port. Uncheck ports that are not connected to port interface boards.
The 'flickering' you're seeing is because the microcontroller input channels are floating inputs by default. They are pulled weakly high by a resistor on the port interface board (or low, if custom interface boards require it).
-Josh