First of all, the Kraken X62 system was intended to control its own radiator fans to regulate CPU chip cooling, but NOT to control the case ventilation fans. A mobo always has at least TWO different cooling control systems. ONE concentrates solely on the CPU chip and uses a temperature sensor built into that chip by its maker to guide it. The Kraken X62 system grabs that temperature readout for its CPU cooling info. The rad fans are totally under control of the Kraken system. It is designed so that, IF it gets NO instructions from the CAM software via the cable connection to a mobo USB2 header, by default it will run the fans at full speed to be sure you get enough (more likely more than enough) cooling of the CPU. Only when the CAM software tool is started does it issue instructions to slow down the rad fans to what is really needed.
Now, it happens that you have also placed both your case ventilation fans under the same control system because you plugged them into the Kraken system. What you really should have done for those two case fans is plug them into your mobo's SYS_FANn headers. These normally use a different temperature sensor built into the mobo as their guide, so they will do slightly different things than the rad fans. Also, connected this way, they will NOT depend on the CAM software; they will be under control of an automatic system built into your mobo. Just to be sure, when you re-connect them to SYS_FAN headers, go into BIOS Setup and see your mobo manual, p. 32, about Smart Fan 5 Settings. Be sure to select the particular SYS_FAN header you have plugged into (don't forget to check BOTH of them) and check the item Fan Control Use Temperature Input. It should be set to the general motherboard temp sensor, not the one inside the CPU chip.