OK, you have provided the explanation. These are 3-pin fans, and apparently the mobo's fan ports are acting like true 3-pin ports. That means that the way they reduce fan speed as necessary is to reduce the voltage supplied to them. BUT you inserted the "low-noise" adapters into each of their power supply lines. What that does is insert a resistor into the line, reducing the fan's voltage even further. Now, a 3-pin fan port knows a couple of important points about those fans. One is, the fan is very poor at starting up at low voltage. So the port always send full voltage to the fan at start-up. A few seconds later, when it has a chance to measure the actual temperature of the items being cooled, it reduces the fan's voltage (and hence speed) until the temperature is under control. From there on it adjusts the fan speed according to the measured temperature. The second thing is, it also knows that such a fan will stall if its supply voltage gets too low, and then the fan will have to wait until the mobo raises the voltage enough to start it up again. So the mobo will never reduce the fan's voltage below a minimum level, to avoid stalling the fan.
What you have done is reduce the voltage more than the mobo intends. So at some point when minimal cooling is needed, the mobo reduces the voltage to its minimum, but the low noise adapter reduces it much further, and the fan stalls. Then you never see it start up again, because the cooling required is not a lot and the voltage is not raised enough to start the fan.
You do not actually need the low noise adapters at all when you connect your fan to the mobo and let it control fan speed automatically. What the automatic control does is constantly measure the temperature at some sensors and adjust fan speed to keep just the right flow of cooling air to maintain the correct temperature. If you use the low noise adapter, what the mobo will do when it needs extra cooling is raise its voltage output enough to get the fan to provide correct cooling. If you leave the adapter out of the line, the result will be the same - the control system will set the fan speed to achieve the same amount of cooling, which means the fan will run at the same speed and be just as quiet. The difference without the low noise adapter is twofold: (a) at high temperatures requiring lots of cooling, the mobo will be able to speed up the fan to full speed if necessary, whereas the use of the adapter would prevent this; and, (b) at low temperatures the mobo can slow the fan down to its minimum speed without stalling it, whereas the use of the adapter causes stalling as you have seen.
Bottom line: remove those low noise adapters and let the mobo do its automatic control properly. It will do a better job of cooling, and it will not cause you any more noise.
FYI, why did the manufacturer supply those low noise adapters? They are intended for use when you connect the fan directly to the full 12 VDC from a PSU output for which there is no automatic speed control. Then you can use the adapter to reduce fan speed and cooling according to your own judgement.