Have you tried choosing "HTML5" from the players list, instead of "Auto"? I don't have the version of Midori in the Trisquel repo, so I can't comfirm it, but I think HTML5 video is supported.

Also, you might want to disable the Netscape plugins in Midori (that's the Totem plugins, Gnash, and all of that kind of stuff). You probably don't really need them, anyway.

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