That cooler comes with TWO cables to make a connection to the mobo for RGB lighting control. That is just to make it easy for you to get it working. BUT you are NOT supposed to try to connect BOTH!
The preferred method is to use the cable with FOUR holes in its connectors on each end. The smaller one goes to the socket on one end of the cooler body, and the larger goes to one of your mobo's two FOUR-pin plain RGB headers. See your mobo manual p. 1-2. items coded 11 at top and bottom edges. Then you use the mobo utility Armoury Crate to control ALL the RGB lights in your system, including those in the Wraith CPU cooler. NOTE that you must plug this in correctly. The connector on the cable has a small triangle near the END to mark the hole for the 12 VDC line. The mobo header has its pins marked and ONE END pin is identified for 12 VDC. You must match these when plugging in!
IF you happen to have a mobo with NO 4-pin plain RGB header (NOT your situation), you do not use that cable. Instead you use the other THREE-pin cable from the 3-pin USB socket on the cooler body to a mobo USB2 header. The you must download and install the Wraith RGB control software, and use that instead of any mobo software to control the Wraith unit's lights.
You are NOT supposed to connect BOTH cables to the Wraith unit. In your case, OP, your better choice is NOT to use the USB cable. Use the 4-pin plain RGB cable to your mobo 4-pin plain RGB header, and use Armoury Crate to control. Do NOT install the Wraith Prism RGB Control software.