As I said, each fan has TWO separate cables. ONE (with a 3-hole fan connector) is for the fan moto. The other (with a wider 4-hole connector) is for the RGB lighting unit in the fan. You say you have connected the four-pin connectors together using some "adapter of the case" to the white RGB header on the mobo near top front. And at one time they worked, but not now. Examine all the connections from fan to adapter to mobo header. It is important that they be plugged in turned the right way. Each connector probably has a mark on it for the pin (or hole) for the 12 VDC power, and those all must match up at each connection point. Then you must have teh Aura Sync software utility (on the mobo's CD) installed and use that to control the lighting.
Completely separate from those lighting cables, each fan has a motor cable ending in a 3-hole female connector, I believe. Your last question may provide a clue. Any cable marked RGB is for the lighting system and needs to go to the mobo RGB header though the adapter. Any fan cable NOT marked RGB probably is the fan MOTOR cable and needs to be connected using the Splitter to your only CHA_FAN header. If your fans are not rugning at all, check all the connections between fans, Splitter and mobo header. You actually have two CHA_FAN headers - one near the front right above the RGB header, and one near the back about half way down the mobo. Whichever one you have the fan motors plugged into, check in BIOS Setup (see p. 3-3 of mobo manual and click on the fan block at bottom centre of the screen) and choose that CHA_FAN header, Make sure it is configured to use Normal automatic speed control, that it is using the DC Mode (not PWM Mode) to control your 3-pin fans, and IF there is a choice, set it to use the temperature sensor on the mobo, not the one inside the CPU chip. After you make any changes, be sure to use the SAVE and EXIT options to get out of Setup and save your new settings.