OK, this makes more sense. With all fans connected to the H100i unit, they ALL are being controlled by the same controller system and temperature sensor, and here is what happens when you first turn on. All fans receive a a signal to run at full speed at start up. This is for two reasons: any fan motor should have nearly full supply voltage just to start it up, but after a few seconds of running it can have a reduced supply to keep running at a lower speed. And more practically, when the system first starts up, the temp sensor and controller system has not yet initiated. Once the mobo has been running for a few seconds and it can get a temp reading from the sensor and process it, it will reduce the CPU_FAN control voltage because the measured CPU temp is low - after all, the unit just started up! After it is running fully, the CPU will start to warm up and the fans will start to speed up to keep the CPU temp under control. But in your case, it's not just the CPU fans - it is ALL of them, because that is how you set your system.
As I said earlier, the idea is that case cooling should be done separately, under control of a different temp sensor in the mobo. That is accomplished only when the case fans are connected to mobo SYS_FAN ports. For that, usually there is no complication, but I'll point out a couple things to watch for.
1. You have two case fans. How many SYS_FAN ports are on your mobo? If you have enough, connect only one fan per port. If not, you can get small adapters to allow connecting 2 fans to one port.
2. On the connectors from the two case fans, how many holes are in the connector end? There are 3-pin and 4-pin fan designs. Similarly, how many pins are on each mobo SYS_FAN port? Ideally, these should match - that is, plug a 3-pin fan into a 3-pin port, and 4-pin to 4-pin. The 4-pin fan design came later and there is backward compatibility designed in, but not perfect. If you connect a 4-pin fan to a 3-pin port, it will work just fine. (Note that the mechanical design of the connectors means that they fit together only one way so you can't do it wrong, and that you CAN plug a 4-pin fan into a 3-pin port.) On the other hand, if you connect a 3-pin fan to a 4-pin port (yes, you can), normally the fan will only run at full speed all the time, and it will NOT be "automatically controlled". I say "normally" because some mobos allow you to manually set a SYS_FAN 4-pin port to perform as a standard 3-pin port if that is the fan you connected, and some even figure this out all by themselves. But not all mobos have these features.
Try connecting your 2 case fans this way. Usually the BIOS default settings will be just fine and you'll get automatic case ventilation fan control without any need to adjust the settings for them.