I don't know if you are using any of the othere RGB headers. I expect that, for the two JRAINBOW headers, you have the option to program each separately or to synchronize them. Within Mystic light I expect that all four of those headers are treated a separate lighting 'channels'. Now, that mobo has two headers for plain RGB called JRGBn, and two for Addressable RGB called JRAINBOWn. That is the tool that sends out control signals from the JRAINBOW1 etc.

(Maybe even uninstall it if this proves right.) The ONLY real way to control the lights in that cooler is to use the utility provided by your mobo maker, the MSI Mystic Light. In that case, the ARGB lighting controller software you get from Cooler Master for the Wraith system is NOT going to work and you can ignore it. Further, that fits only onto one of the two mobo headers marked JRAINBOW1 or. To be sure, I expect that looks like it has space for 4 holes, but one is blocked off. So the Wraith cooler you have is a different version that has ONLY one cable to plug into a mobo header, and it has THREE holes, right. You may well be using that utility anyway for other lights.

You use the utility that comes with your MSI mobo to control RGB lights from the header. Then you don't need the Cooler Master utility, nor the USB cable connection. In doing that last connection, you MUST get the polarity right The connector has a mark on one end to mark the +12 VDC line, and that must mate with the correct pin of the header which also should have a 12 VDC marker. IF you want to do it the other way, you connect the 4-hole cable to the 4-pin socket on the Wraith, and then plug the other end of that with 4 holes in a larger connector into one of your mobo's 4-pin plain RGB headers.

To use the Cooler Master version of the Wraith RGB control system, you should connect ONLY the cable with a THREE-hole connector on one end (to the 3-pin socket) and then the larger connector on the other end goes to a USB2 header on your mobo.

According to the video I saw (check your Wraith manual), you are to connect only ONE of these when you decide how to power and control its lights. The Prism body has two sockets on its side - one 3-pin, one 4-pin - and it comes with two cables.

Wraith prism rgb control