Let's assume your description is all correct. Then what I expect is happening is that the Hub is a LIGHTING Hub only (does not do any fan speed control). The TOP 2-pin connector and cable go to the LED control switch supplied with the case, and that's how you can change the displays manually. The BOTTOM connector has two 2-wire connections, and you say one pair goes to a SATA power connector that you say is NOT connected to anything. It should be plugged into a SATA power output connector from the PSU to provide power for all the fan lights. The other pair goes to the mobo JRAINBOW header, and that is so that header (and the utility supplied with your MSI mobo) can control the display INSTEAD of the manual button.
Go back to your case installation / user instructions about this Hub. MANY such systems default to using the manual button for control, but allow you to switch to let the mobo signal take over. The METHOD of switching is what you need. Often it is simply to push and hold down the manual button for 5 sec or longer.