Comment 7 for bug 535426

I repeated the same steps, it doesn't flicker with "gst-launch-0.10 playbin2".
It's probably connected to the "selected widget indication". If the drop down menu above the playlist is selected, it turns orange. If you focus another window, the orange highlight disappears. I suspect that the same thing is happening when the video area is selected. If the totem window loses focus, the (in this case not visible) "widget indication" goes away, which causes a short flicker.