rjmoerland,

Your issue is basically the same as what I've been experiencing.

Frankly, I'm surprised that more Ubuntu users are not reporting this
issue on launchpad.  Maybe it's because they don't even know about
launchpad.

I believe this problem is not caused by vlc 0.9.4 , but possibly from OS
changes that occured between Ubuntu 8.04 to Ubuntu 8.10.   Why do I
believe this?  I've observed random stalling/skipping while audio
continues while troubleshooting this issue in both Ubuntu packages vlc
0.8.6h and 0.9.4

Usually what happens is a reboot or system change will make the random
skipping go away for a short period of time only to return shortly
after.  Some changes like unchecking vlc's disable screensaver option
improved the visibility of  random skipping the problem, but it still
resides if you look hard enough.

You can see in the forum threads below where I tried many different
things hoping to find a workaround.  I've tested the following
configurations with no change.

VLC: 0.8.6h/0.9.4
Compiz: On/Off
Video Output Module: X11/XVideo
VLC Disable Screensaver: On/Off


Below are some threads of users reporting this issue (there may be more threads)

http://ubuntuforums.org/showthread.php?t=1000393
http://ubuntuforums.org/showthread.php?t=972696

http://forum.videolan.org/viewtopic.php?f=13&t=53160
http://forum.videolan.org/viewtopic.php?f=13&t=53415

One observation I've noted in my posts is that this random frame
skipping always coincides with a CPU spike in Xorg as well as gnome-
screensaver (when VLC disable screensaver option is enabled).  This can
be seen by opening a terminal window, running the top command, then
starting a video in vlc.  Wait for random skipping to occur in vlc, when
it happens, look at top output and there should be a 10% spike in xorg
right as it happens.

I believe the observed effects of this bug may be related to a Xorg bug
although I can not say if this is certain.  All I know for sure is that
this random frame skipping coincides with a CPU spike in Xorg.

https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/294972

-- 
vlc 0.9.4 slower than 0.8.6 - video freezes then resumes pixelated for a few 
seconds
https://bugs.launchpad.net/bugs/308385
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