ASUS M4A89GTD PRO/USB3 motherboard with on-board Realtek HD audio ALC892, and AMD's Phenom II X6 1090T processor, connected via optical audio cable (a.k.a. Tosklink) to a Bose Lifestyle 28 Series 1 Home Theater System.  Windows 7 64-bit OS installed.  ASUS motherboard support disc was originally used to install Realtek HD Audio driver version R2.54.

Sound from the optical output of the motherboard has crackle and pop noises..  These noise defects are particularly noticeable when playing quiet music tracks like the Bob Acri jazz track included with Windows 7 through Windows Media Player 12.

When playing an .mpg video, or a DVD through Windows Media Player 12 in Windows7 64-bit, there is approximately a 1sec delay between when the video starts, and the audio starts.  Every time I change to a new .mpg, or a new DVD menu or chapter, it takes about 1 second before the sound starts playing.  It is not an audio sync delay, but rather a delay between when the video started, and when the audio stream could be heard. 

If I play the same video through VLC media player, it has no delay, so it is an issue related specifically to Windows Media Player.  Also, there is no delay with mp3 music files or .avi movies played through Windows Media Player, so it is only an issue with the .mpg and DVD file type encoding.

Install the latest Realtek HD audio driver from the Realtek website (R2.55 or higher).  The updated driver fixes the snap, crackle, pop noises.  Simply go to www.realtek.com, then "Downloads," then "High Definition Audio Codecs (Software)." 

Just get the Executable file labeled for your operating system.  For Example "Vista, Windows7 Driver (32/64 bits) Driver Only (Executable File)."  (Click on the screenshot to the right to see an example of the Realtek downloads page ►).  After downloading, just click on that executable file and follow the instructions to update your driver.  You will have to restart your computer.

(Credit for this solution belongs to Markus Hedlund, as detailed in his article here.)

Even though not related to this issue at all, while you're at Realtek.com, go ahead and get the latest "Ati HDMI Audio Device" driver, too.  It might be at a different rev than the HD Audio Driver.  At the time of this writing, it was still at R2.55, while the regular HD Audio driver was at R2.58 ►.

Other notes: I have had a couple other times when the sound from my optical output has sounded bad, like electronic noise overlayed over the music.  That was solved simply by restarting the computer.

I solved the WMP12 movie sound delay issue by changing a setting for the Optical Output Device.  Right click on the little white speaker in the taskbar, and then click "Playback Devices."  Click on the "Realtek Digital Output(Optical)" device, then go to the Advanced tab and deselect the "Allow applications to take exclusive control of this device."

Apparently WMP likes to take exclusive control, but induces that 1 second delay every time you switch between .mpg files, or when you skip chapters on a DVD.  The delay seems to be because of WMP negotiating control of the device each time.  Turning off that setting solves the problem.  As a side note, I also noticed that when it was allowed to take control, certain DVD files would also not allow their volumes to be controlled by either the WMP volume slider, or the computer volume slider....and the output of the movie was quieter than normal.  Turning off the "exclusive control" setting I mentioned solved those problems, too.

WHEN YOU UPDATE YOUR DRIVER, you have to uncheck this box again.  Writing this edit on 9/22/12, I just updated to Realtek driver v2.70, and found that I had to go back and uncheck that box again because when the driver was updated, it reset all of the properties back to default.