Greetings,
I'm using 3 pin fans everywhere except the CPU. I have SIV installed, but do not use SMART Fan, all fan control is done in BIOS. I find this to be the most reliable.
I think it was wise to uninstall any power management or fan related profiles from the OS, but I've seen lingering issues result when people create BIOS profiles and/or use SMART Fan to management fans (even after profiles are removed, or software is uninstalled).
If you are using any type of fan controller module, or are using any "Y" adapters (or molex) this too has been known to cause issues. Fans should be connected directly to a MB's fan header., no adapters for best results.
Note: the board calls for a 500watt PSU minimum (recommended). That's not to say it won't run on less, but 300w is pushing it.
Steps I might take:
(After confirming all fans are connected directly to the board)
-Reset BIOS to defaults, changing only what is needed for the system to boot - test the fan behavior
-If 2 similar fans are installed switch connections and see if the behavior follows, if so, replace the fan having issues
-Test with more powerful PSU
Things I wouldn't do:
-Continue updating my BIOS
-Your CPU requires F40, continuing to update just for the sake of being current, might not be best
In some cases BIOS updates can help and are indicated, but things can also get kludgy when you are running a BIOS intended for a newer CPU / chipset / FW and the CPU you have installed is one or more generations behind.(Just be mindful of this).
**One last thing. If it's possible to modify the RPM threshold in BIOS, this too might be an option for you.