Fan makes my Motherboard hot!!

Asus P5B Deluxe. I have been changing to watercooling and noticed a fair amount of strange happenings. For instance 100ml extra of coolant takes the temp down by about 5 degrees. One you may be able to help me with. I have just added 2x Noctua NF-S12 800s to the front of the case and they are brilliant. I disconnected my thermaltake i12 at the rear of the case and the temp reached 31deg on the CPU and 30 on the mobo. So I thought lets see what difference adding the thermaltake back on brings. Answer.....the bobo temp increased by 2 degrees. Is this about current draw or anything else? Help if you can please as I am totally confuzzled