I know what to think then, other than it might be faulty machine. If the macbook was older (5+ years) , I guess you could expect problems like that), but it should still work pretty well at two years. After all, it's mac!
Maybe if it would be possible for you to post up a video, it might be easier for me to help. Does this problem make your machine totally unusable? Also, does it occur all time or just out of the blue sometimes?
One thing to get straight, this only happens when you have windows open, not when everything is closed or minimized and you can see the desktop.