Your mobo and CPU are just fine You DO have a problem with that CPU cooling fan, though. I suspect its bearings are wearing out, so it is time to replace it. Just the fan needs replacing - NOT the entire CPU cooling system.
This is what I think is happening. On any system when you first turn it on, the voltage to the fan rises from zero to full +12 VDC, and it starts up. As the mobo completes its start-up sequence, its automatic CPU fan speed control system acquires a temperature signal from the sensor inside the CPU and uses it to determine what speed that fan should run. When it realizes that the CPU temp is low (it has only just started to work!) it reduces the fan voltage and the fan slows down.
In your case, worn fan bearings make it hard to start at first, but soon it does start up. The noise you hear then is the fan shaft rattling around in a loose bearing. The noise reduces as the fan speed is reduced after a few seconds.
If you do nothing, this will continue to get worse until the fan quits altogether, risking damage your CPU. So replace it now while it is still working.