Sorry should have included that, yes I have a total of 6 Corsiar LL's in the case, 2 on the H100i and 4 of them are hooked into the Commander Pro now.
Prior to this I had the Lighting Node Pro and at that time my H100i fans *were* connected through the power connectors on the pump, but I got got confused when the mobo starting throwing the error about the empty CPU fan controller.
Your context and the info provided by c-attack below clarified this for me. My bios info was telling me to do exactly what c-attack was saying ( disable the error messaging ) but it sounds like you both recommend keeping the power connected to the pump connections like I had it originally. I'll do that and report back for the sake of anyone else asking similar questions in the future. Many thanks.