> I don't think it has to do with Flash since the same video runs fine
in the other operating system but not in Ubuntu.

They support hw acceleration on Linux for anything other than the nvidia
propietary drivers. (Well at one point they had support for Intel PVR
chips...) As far as I am aware we (Intel) have not made any inroads into
getting them to support more hw.

> Also, the same problem occurs for html5 videos which I think, correct
me if I'm wrong, is open source on youtube.

If you are referring to chrome, then it is about as open source as code
dumps many months after the fact can be... But we are working with them.
WebKit itself seems to drift along  failing to get acceleration to work,
as the original code base is completely adverse to GPU acceleration.
(And our efforts here are sadly not aimed at the desktop.) Firefox
should pick up support through gstreamer, eventually.

Thinking about the skips:

Can you switch to a console with CRTL-ATL-F2, login and stop lightdm
(sudo service lightdm stop). Then launch X and start playback:

$ sudo Xorg -ac -noreset :0 & sleep 5 ; DISPLAY=:0 mplayer -fs
'/home/user/Downloads/Crossroads: Labor Pains of a New Worldview | FULL
MOVIE.mp4'

Does it ever skip then?

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https://bugs.launchpad.net/bugs/1103236

Title:
  Choppy and pixelated video on Macbook Air 5,1. Unable to run/view HD
  videos at all

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