Are you all absolutely sure you're not confusing the fan's sound with the disc drive's sound? The fan is normally very quiet, almost unnoticeable during play, it's the disc drive that makes all the noise. That'd explain the confusing report about the fan turning off when loading the Homebrew Channel... because at that point, the disc drive stops spinning as well!
Plus, the fan's simply not handled by IOS. The fan runs even when no IOS is active (BootMii, or even when you delete all IOS), because it's hardware-controlled.
Please don't flame me, exactly the same mistake has happened in these forums before!