What are you exact hardware specs including motherboard model, CPU, CPU cooler, case, case fan model(s), case fan population locations, whether a fan hub is in use, GPU model, etc?
Are you certain that it's "a few minutes" and not more like a few seconds? Do the fans slow back down as soon as you clear POST and begin to boot into Windows?
Did they work normally all the time before and only suddenly begin acting different or have they acted this way for the entire time you've had the fans set to quiet mode?