I'm having the same problem since Youtube changed to the new design (and also HTML5 coding?) a couple of weeks ago. Also noticed that I can no longer download the video using the activity monitor since it apparently streams the vid (?).
The video lag is terrible (on my brand new iMac) with QTKitServer process above 100% and Safari lagging like hell, often with baseball mouse icon, all for about 48 seconds. When I switch resolutions, it starts all over. Sound however plays fine with few sporadic stuttering.
Software is all up to date, including Flash (just in case).
Anyone has any idea wtf could be done? Youtube is a pita to use this way