When i mount my engine directly to the command disc, fuel flows through the disc from a tank on the other side. However when i sandwich the command disc between two fuel tanks, it no longer lets fuel flow through it.
To reproduce, create a craft like the attached. Observe how the top tank does not autofill with fuel, and even if you force the fuel type it will not be utilized.
Remove the bottom tank from the stack and see how the behavior in the top tank is different.