This had been bugging me for several months. Symptom was intermittent (every few minutes) skips/dropouts in the onboard audio on an Asus M5A97 running Ubuntu Linux. They're very short (just a fraction of a second), but quite annoying.
Building the latest Realtek drivers from the source code posted on their web site did not help.
Turns out there's a problem with Realtek's front headphone jack sensing in Linux, which causes the system to randomly cut off the audio outputs on the rear I/O cluster because it (incorrectly) thinks you've plugged something into the front headphone jack. Several people at the end of this thread on the Arch Linux forums were experiencing similar issues.
The workaround is to use the AlsaMixer tool to disable Auto-Mute. And yes, this does mean you need to remember to turn down (or off) your speakers whenever you plug your headphones into the front panel jack, since the main outputs will stay on all the time instead of automatically shutting off.