The three SYS_FAN headers on your mobo may have 4 pins, but they actually appear (according to the labels on p. 1-22 of it manual) to be operating in Voltage Control Mode only, which is exactly what is needed to power and control 3-pin fans. HOWEVER, you have caused your own problem.
Those "cable adapters" that come with your fans are NOT supposed to be used when you connect them to a mobo header that automatically control a fan's speed. They are used only when you connect the fans directly to a fixed 12 VDC supply from the PSU and have no other way to control the fan's speed. Each adapter is a small resistor that reduces the voltage going to the fan, so using them with a fixed 12 VDC supply allows you to reduce their speed. BUT you are connecting your fans to mobo SYS_FAN headers and they control the speed of their fans by reducing the voltage sent out. By using those adapters in addition to the reduced voltage from the mobo header, you are supplying those fans with a voltage so low that at least one of them cannot start up without help.
Remove all of those those "low noise" adapters from the leads to your fans. See your manual, p. 3-28. For each of your fans (3 SYS_FANs and the CPU_FAN), ensure that they are set to use the "Smart Fan Mode". Then for each, ensure that the "All Set Default" choice has been chosen. When done, back out of BIOS Setup and don't forget to SAVE and EXIT. What the mobo fan headers will do when set this way is to check constantly the temperatures measured by two sensors (one inside the CPU chip, and one on the mobo) and adjust their respective fans' speeds to make sure the actual temperatures are what they should be. If your system is running cool, it will slow the fans down and they will be quieter; if temperatures rise, the fans will speed up. You do NOT want to defeat all that by forcing the fans to be slow and quiet all the time, because then you are preventing proper cooling of your system.
I'm confused about your CPU cooling fans. You seem to say you have one 4-pin fan on the CPU plugged into the mobo CPU_FAN header, PLUS a second fan - this one 3-pin type - cooling the CPU and plugged into a "4-pin slot" you don't identify. Is that correct? Your CPU_FAN headers DO use PWM Mode for control (and only that mode I think), so each can control a 4-pin fan properly. But if you connect a 3-pin fan to such a header (in your case, either CPU_FAN1 or 2) there is no speed control - that 3-pin fan can only run at full speed all the time. So, do you have a 3-pin fan plugged into one of those CPU_FANn headers? If you do, I expect that fan's speed is NOT ever going to be less than full speed. If that is the case, this is the ONE place where you could afford to use one of those "Low Noise Adapters" in the cable to that 3-pin fan, since it is receiving a fixed 12 VDC supply from a mobo header that is trying to use PWM Mode to control a 4-pin fan that isn't.