This is a copy/paste of a bug report i first submitted to mplayer2 developers, here:
http://devel.mplayer2.org/ticket/67

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Using Linux 2.6.39 with ion hardware and mplayer2 from archlinux packages, i found an h264 stream that, if decoded in hardware using mplayer2, exposes several video glitches.
I remuxed from mkv to avi, but things remains the same.

* Please note that the same file played with vlc exposes the same glitches. *

While if played with xbmc,with mplayer (1), and with mplayer-vaapi(with vdpau backend) (all those still hardware decoded) is perfectly fine.
Decoding it in software also plays without issue, even with vdpau output driver.

Here are two links for the video stream:
http://wpage.unina.it/aorefice/sharevari/vdpau/glitch.at.second_6.mkv
http://wpage.unina.it/aorefice/sharevari/vdpau/glitch.at.second_6.avi

Here are two screenshots; the first is the file decoded by mplayer2
the second is the same decoded with mplayer(1) with the same options.
http://wpage.unina.it/aorefice/sharevari/vdpau/mplayer2_glitch.png
http://wpage.unina.it/aorefice/sharevari/vdpau/mplayer1_noglitch.png
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However the bug has been marked as invalid because it seems that mplayer2 was linked versus a buggy libavcodec.

It should be sufficient to rebuild mplayer2 on a recent liavcodec version.