This seems to be a problem with Flash on Firefox, if you force the YouTube player HTML5, the problem is fixed.
http://jsfiddle.net/8EMzc/
Do this by adding the URL &html5=1 to YouTube. I believe that if HTML5 is not supported, it will revert to Flash, but I'm not sure about that. You can also hack the browser and use the HTML5 player only for Firefox (not recommended, but you are working with an error, so there is no easy way to solve this problem).
Alternatively, you can turn off CSS transforms in Isotope with the transformsEnabled option
$('#container').isotope({ transformsEnabled : false });
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