Motherboard temp #2 is likely your CPU socket. If your thermal paste is good I would say that your H100i is not doing its job.
Try the stock cooler if you still have it just to see the difference.
Looking like that so far, although just tried messing with the pump settings again and got the same results so I'm not sure. When I decrease the pump amount, temperature raises significantly faster. When I increase it, temperature drops for a couple degrees and then continues its climb