Hi there. I have an DX58SO Motherboard and the same problem. Everytime when I start the computer the fans run on full speed but before booting they slow down to lower speeds. But not everytime, sometimes they are not controlled and they run on full speed all the time (also in Windows). When I reset the computer (I mean the hardware reset switch), the fans runs slower, quiter (sometimes on the 2nd try). Don't someone know where can be the problem ? Everything works fine, my BIOS is latest, but the problem occurs often.
The solution to your problem is to let the power to your unit remain plugged in with the PSU switch always on. Use the computer front power button to switch on the unit and your OS to shut it down. This is discussed in this link. It is a hardware problem but which I consider to be tolerablel.