Ah, I partly misunderstood.
The IntelliComm II is indeed supposed to be able to draw power from the Hayward communications line pins 1 and 4 (red and green respectively).
I can think of a few reasons that wouldn't work. One would be if you accidentally wired it to some other pins, perhaps if the wire colors did not match up with their conventional pin numbers. The other would be if the OnCommand does not have enough power available on the comm pins for everything that is attached to them. It should have enough power for the IntelliComm II alone, but if additional devices drawing power were also attached there is some chance the total power could exceed it's capacity. The final possibility is if there is a short somewhere in your IntelliComm II connections, so that connecting the red wire somehow shorts the red wire to something else that is connected to ground on the OnCommand.