EDIT: The answer from @Archer seems to fix it. (please vote for him, because I do not have enough points for this).
To learn more about the error, click here: http://www.viget.com/inspire/webkit-transform-kill-the-flash/
My problem is not easy to explain. I compiled a test case on jsfiddle. You can find the link at the bottom of this text.
Before you click on the demo link, pay attention to the following:
Make sure you are using Google Chrome. (due to -webkit CSS prefixes).
Pay attention to the first time you press the orange button. Before starting the animation, you should see a short flash. When you try again (after pressing the reset button) everything will be fine, there is no blinking screen. But if you clear the browser cache (CTRL-SHIFT-DEL), close the browser and reload the page, hiccups will appear again.
I hope I have clearly explained this.
DEMO: http://jsfiddle.net/NKQNX/14/
(sorry for my spelling, English is not my first language)
The robster
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