Hi, I'm having this problem too, after upgrading from Lucid to Maverick. 
Tried to install newer alsa drivers from alsa site, but somehow it didn't 
worked (I hadn't sound at all), so I restored default Ubuntu configuration. 

Just added "options snd-hda-intel model=intel-alc889a" to
/etc/modprobe.d/alsa-base.conf

Now, I've tried to compile kernel from linux-source with the same modules 
currently installed and the issue persisted.
I have seen in both cases this kind of output in /var/log/messages when skips 
occur:

Feb  3 00:38:53 PHENIIX4TMP1 pulseaudio[2372]: ratelimit.c: 20 events
suppressed

This is with kernel 2.6.35-25.
I've installed a newer kernel from Ubuntu Kernel team, 2.6.35-26, and now there 
are less pulseaudio logs, but the issues(skips) are still present.

I've tried with mp3, wma and m4a (verified) files and youtube vids., and all of 
them have the same problem.
I have even tried aplay /usr/share/sounds/KDE-Im-Phone-Ring.wav and I got 4 
pulseaudio lines (and their respective skips)! 
So it can't be related to decoders. That wav file had 4 skips during its about 
2 seconds playback.

Kubuntu 10.10 Maverick x86_64, kernel 2.6.35-25, 2.6.35-26.
fglrx Version: 2:8.780-0ubuntu2

Phenom II 955BE (@3.2GHz, Stock Freq.), 
Motherboard GIGABYTE GA-MA790FXT-UD5P
Chipset AMD 790FX  + AMD SB750 
Realtek ALC889A codec (Detected as "tarjeta 0: SB [HDA ATI SB], dispositivo 0: 
ALC889A Analog [ALC889A Analog]" by aplay)
8 GB DDR3 RAM.
Graphics card: MSI ATI Radeon HD4830

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https://bugs.launchpad.net/bugs/587185

Title:
  [Realtek ALC889A] Playback problem,  stuttering audio & video

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