This is an info thread on how to solve an issue with Realtek AC97 / High Definition Audio sound cards. I'm using an Asus P5N-D and after installing the drivers for the sound card, I noticed a high pitch noise coming from my speakers, which made no sense because it only started coming on when Windows was loading. I originaly suspected bad hardware or bad drivers, but turns out its a setting issue with the Realtek Audio Manager. There is an option for something called "PC Beep" which causes the noise. All you need to do is mute it and the noise should go away.
For Asus motherboard users, here are the steps for muting the "PC Beep":
1.) Install the Realtek Audio Manager (comes with the motherboard drivers usually)
2.) In Windows, open up the Realtek Audio Manager and click on the Mixer tab.
3.) Scroll forward under Playback section until you see the "PC Beep" option, then Mute.