jossrik is correct. The Phanteks PWM Hub included in your case is a unique hub because it uses one PWM fan control signal from a mobo SYS_FAN port to create six of its own 3-pin Voltage Control Mode ports for fans. Now, fan design is such that both 3-pin and 4-pin fans CAN be controlled by such a system, so that any fan plugged into the Hub should be under mobo control. You really should make sure that one fan is plugged into the Hub's white Port #1 - that is the only port that sends a fan speed signal back to the mobo. If there's no fan on that port, your BIOS will alarm you that the case ventilation fans has failed.
HOWEVER, to make this work you must connect it correctly. The Hub has two connection cables to it. One goes to a SATA power output connector from the PSU to get all the power for the Hub's fans. The other is a normal female 4-pin fan connector that MUST be plugged into a mobo port that actually supplies a PWM signal. And HERE is likely your problem! I am assuming that you have plugged this Hub connector into one mobo SYS_FAN port. BUT in your mobo's manual, page 3-43 Chassis Fan 1/2/3/4/ Q-Fan Control, it says there are three options to choose and by default it comes set to DC Mode. This is WRONG for what you are doing. Make sure you set this BIOS item for the port you are using to PWM Mode. Then remember to SAVE and EXIT to keep that setting. That should give your Hub the required PWM signal to control all the case fans plugged into it.