When my system starts, the fastest fan can not get past 1200-1300 rpm so is considered more quiet then having a 2000rpm fan run full speed.
If you can live with one speed or manual speed control, you can use a fan controller(or 5 volt mod some fans ) to set the speed once and it will always run that way.
This is not always recommended for cpu fans as with the board in control at least if it gets too hot, it will crank the fans up, while if you set it too low it can overheat with the board not being able to auto control the speed.
That being said, some heatsinks are more then capable of low speed cooling.
I think you may be stuck with it. Unless you want to control then another way.
Just as an example, on my Antec 900 case, I ran all the fans on low(but they have a control switch) so they just ran at that speed all the time.
You can get a fan controller(some fit in the CD bay or even in a rear pci slot) to run them at a lower speed.
They also sell cables to drop the voltage to 5 volts(its just a molex using the red wire as opposed to the yellow wire.). 7 volt adapters exist as well(red to yellow), but users have mixed feelings on that idea.
amuffin, with it running full out then dropping, I do not think they will find a bios fix for it.