Check some of these settings on the headers your fans use.
CHA_FAN1 / WP Switch set to PUMP, and Temp Source set to Monitor CPU. This ensures the AIO pump connected there will always run full speed as designed.
CPU_FAN1 you may have no options to adjust, other than setting to Silent Mode for a pre-set low-speed fan curve as you have done.
CHA_FAN2 (and 3 and 4 - set all of these the same):
All should have the Switch set to Fan, not Pump
Control Mode set to PWM assuming your fans are 4-pin type
Setting to Silent or Customize or whichever Profile you want.
Temp Source to Monitor MB, not to CPU. THIS may be why ALL your fans are doing the same thing IF you have these case fan headers controlled by the temp sensor inside the CPU.
The fact the speed reading on CPU_FAN1 disappears randomly will NOT affect the mobo's ability to control that fan. But it MIGHT be a hint about the quick change of fan speed. For any fan header that signal is monitored to detect FAILURE by getting NO fan speed. Normally the automatic reaction of the header to a failure is to change the speed setting to full speed to ensure the fan really does start up, then watch for a good speed signal. IF the speed signal is restored then the fan speed signal is returned to whatever it was before. However, if that signal is set so low that it actually caused the fan to stall, the whole process will repeat continuously. On the other hand, if the speed signal does NOT come back under a full-speed signal condition, the header will pop up a screen warning of fan failure and, in the case of the CPU_FAN headers, take more drastic action to shut down your whole system to protect the CPU from damage by overheating due to NO cooling. You do NOT report such warnings or any shut-down, so we should assume that any actual fan stall IS recovered by the automatic re-start process.
That leaves us with the question: Does at least ONE of the three fans daisy-chained on the CPU_FAN1 header actually stall and trigger this process, repeating that sequence? YOU need to watch the actual fan action, NOT just look at the screen display of fan speed, to check this. IF the one fan of that trio is somehow stalling, it is possible that the Quiet pre-set fan curve you are using is set too go too slow at low temperatures and causing the fan stall. For that you would need to alter the fan speed setting at the lowest temperatures.
Another thing to check in that group. You have three fans connected in a daisy-chain system to the CPU_FAN1 header. Only ONE of those (quite likely the first in the chain) can report its speed back to the header. So two items might cause a bad speed signal there. ONE is that the connection from the first fan back to the header is faulty or dirty. So try this with your system shut down completely and unplugged from the wall. At each end of that cable from the header to the first fan, disconnect the cable, then re-connect it. Do this several times. This action may "scrub" any dirt or oxidation from the contacts in the connectors. Re-connect everything, plug your machine back into the wall, and try how it works.
Another possibility is that the cables are OK, but the one fan whose speed signal is sent back to the header (probably first in the daisy chain) is failing to send its signal. Try re-arranging the cables between the three fans so that first fan is last in the connection sequence and a new fan of those three is now the only one sending back its speed signal. See if that makes a difference.