While I am not really into this video stuff even though I own a 5DmkII, I have read that sometimes different video players do better than others. A recent post I read somewhere even stated that Quicktime was not so good with these Canon flicks. I played the DPR .mov and opened it in Windows Media Player and it ran fine but it looks to be a handheld shoot and that part is jerky.
What few videos I have shot have always been smooth playing albeit jerky hand held cinema photography. I have a 2.4 ghz computer with fairly good graphic card.