I recently built a new machine for work and was having a lot of issues with audio (on linux, what a shock ;)). I’d read up on some different fixes and none of them seemed to fix the issues I was having with my system. After about a week of woes and a lack of music I decided to open up the box and swap the audio cable from HD to AC97 just to see if it might fix the issue. Low and behold audio plays fine without issue using the older standard. I don’t reap the benefits of HD audio, but not being an audiophile and working with middle of the road headphones I can’t tell a difference anyways.
So just a heads up, if software can’t fix your skipping audio, maybe give your hardware a try.