First thing I suggest is that you boot directly into BIOS Setup and go to the main Monitor Menu - see manual p. 2-34. Check there for the temperatures of your CPU and Motherboard. These numbers are reliable. IF they agree with your Speedfan indications of some temp in the 125 degree range, then you know you do have something wrong. On the other hand, if they do NOT show such problems, then Speedfan may be wrong. In that latter case, you might need to seek advice from Speedfan or from others here about how to correct Speedfan's actions.
If the BIOS screen does show a very high temp somewhere, you certainly need to investigate what that item is, and why it is hot. But if not, then we look elsewhere.
Interestingly, the manual indicates that the mobo itself has only two temperature sensors - the one inside the CPU chip, and one installed on the mobo. There are no other sensors available for your BIOS to show, so what Speedfan is reporting as "AUXTIN0 and ...3 is not clear. It MAY be reporting non-existent readings that do NOT pertain to your mobo and should be ignored and maybe Disabled if they can be.
Now, the warning noise comes even when Speedfan is not running, you say, so we can conclude that the sounds are being generated by your mobo BIOS. In the manual on p. 2-35 I see four items you can set that generate warning alarms. Each is related to the minimum speed of a fan - one for the CPU fan, and one for each of the three CHA_FAN headers. There are few other possibilities, too, I'll note later. The CPU Fan Speed Low Limit is set by default to 600 RPM, but many current fans do operate properly at lower speeds. If possible, see if you can find the specs for your CPU cooling fan and see what its minimum speed should be. Also observe what speed it really is running shortly after you start up while the CPU is cool. If that is lower than the current limit setting, that is what is causing your warning sound. You can change that limit setting according to what speed the fan really DOES run in the cool system, or according to its min speed spec. The function of this Limit setting is to detect FAILURE of that fan and send out a warning you cannot ignore (It's working now!), but it is not part of fan speed control. So it should be set to below any normal speed for that fan.
Very similarly, look at the items for each of your CHA_FAN headers. They each have their own minimum fan limit that can cause an alarm, and again the default 600 RPM setting may not suit your actual fans. In these CHA_FAN headers, also note in the min speed limit setting that there is an option to IGNORE which you should choose for any fan header that is NOT being used for a fan. (Don't choose that for the CPU_FAN header, though.)
Now, for the CPU_FAN and all of the CHA_FAN headers one choice of Profile is "Manual". In that mode, you get to specify your own fan response settings. That is, what is the correct minimum fan speed at a minimum temperature you select, and what is the max speed at what max temperature? You also get to specify the slowest fan speed control setting (in terms of "Duty Cycle"), which is not exactly a specific speed. IF you have NOT chosen this Manual Profile, then the options for these items will not be shown and you can ignore them.
So, check into those fan speed limit settings. THEY may be what is causing your alarm sounds, and they may be wrong and require re-configuration. But all that depends FIRST on checking to verify that actual important temperatures are NOT too high and you can stop worrying about the temps.