I assume you already have but it might be worth checking again to ensure the backplane is aligned correctly and firmly on the Controller board (both 2x10 and 2x3 headers) and similarly the Pi are aligned and firmly located in the backplane.
With power applied to the ClusterCTRL Stack After running "clusterctrl on" do you see all p1-p5 set to 1 in "clusterctrl status" output?
If so then it's unlikely to be a software/firmware issue - on the ClusterCTRL Stack the firmware reads the status from the GPIO register so if it thinks the pin is high then the pin should be high.
The control path out of the ATmega328 then goes to the MOSFET U2 for P1 through U6 for P5 next to the 2x10 header which control power.
If you have a multimeter you could carefully check the voltage on the 2x10 header after running "clusterctrl on". Each Pi has 4 pins, the two closest to the mounting hole are 5V for P1 and then going towards the 2x3 header they alternate GND, 5V(P2), GND, 5V(P3), GND, etc. You might find it easier to check voltage by holding the negative of the meter on the USB Type-A socket (it's connected to GND) and then tap the positive of the meter on the pin closest to the edge of the board being careful not to short the pins as this may cause damage.
Chris.