deimos3428 has the key first part of your answer. With the CPU cooler plugged into the mobo port, its speed is controlled by the BIOS CPU cooler control system. Its action, quite reasonably, is to run the fan at full speed when first turned on and wait until the temperature signal from the CPU's sensor yields a reliable stable reading. Then it reduces that fan speed to keep the CPU at the temp you set. It just happens by coincidence that the CPU temp signal stabilizes at about the same time that Windows finishes loading. I bet the fan speed is controlled by the BIOS, not Windows or any application running under Windows. (A lot of critics would tell you that letting Windows control something as critical as the CPU temperature is too risky and a waste of OS resources.)
The other concern you have is the temperature that it seems to settle at - you think it is too high. Maybe it is, maybe not - I don't know. But the CPU manufacturers probably have recommended operating temps for your unit. The question is, should you decide it is necessary, how do you change what you have now? One way is to give up on the CPU fan speed control system and just run it full-on and get as cool as possible, and that might be necessary. The other way is to adjust the parameters of the fan speed control to achieve the same end, but under automated control that can adjust to changes. I don't know your system, but check into its manual for starters. On my mobo within the BIOS Setup screens under the heading "Hardware Monitor" for the CPU cooling control, I can set three parameters - temperatures, actually. At some low temp the fan will first start to run slowly. At some high temp it will run at full speed, and in between those temps its speed will be linearly related to the temperature. At a higher temperature yet the BIOS will change the clock speed to slow the whole system down and reduce heat generation. There's a fourth parameter I can't adjust, the temperature at which the whole system will shut down to stop heat generation completely and protect the CPU from catastrophe. Of course, the BIOS uses its default values until you change them, and that's how you get the temperatures you are seeing now. See if you have some similar way of adjusting your system to run the fan faster under "normal" conditions and give you the CPU temperature you decide you want to see. I am guessing that your BIOS is doing something like this, and the Easy Tune 6 utility is just the easy way to make those customized adjustments of many BIOS settings, including temperature control.
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