All of this depends on which mobo headers you have plugged the various fans into, AND on whether they are set (IF they can be) to match the needs of the different fan types. To help with that, we need to know the exact maker and model number of your mobo.
For starters, here is how the H100i system is supposed to be connected, so check that it is this way.
1. The H100i's PUMP unit has two cables coming from it, and sockets for two more cables. One cable ends in a 3-pin female (with 3 holes) fan connector that should plug into the mobo CPU_FAN header. This can feed the pump speed signal to that header. The second cable ends in a wide connector that must plug into a SATA power output connector from the PSU, to supply power to the entire H100i system. The system comes with a fan splitter cable that plugs into a socket on the pump, and then BOTH of the radiator fans must plug into this cable, not into any mobo header. Finally, there is a cable to connect from a pump socket to a mobo USB2 header so that the Corsair Link software, once installed, can control all the system speeds and display them for you.
Set up this way, AISuite will tell you that the device connected to the CPU_FAN header has a certain speed. But that is the speed of the PUMP, which has been set by Corsair Link to run at full speed (2800 rpm) all the time. The only way to tell the FAN speeds on the radiator is to use Corsair Link to see them, and there you will see their speeds change according to system workload.
Corsair AF120 Performance Edition fans that you are using for case ventilation are of the 3-pin design. This means that the ONLY way to control their speeds is using Voltage Control Mode (aka DC Mode). PWM Mode headers will cause these fans to run all the time a their full speed, which appears to be what you observe. If you tell us what mobo you have, we can advise whether (and how) you can get your mobo headers to control their speeds. If they cannot, there are other ways we can suggest.
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