I need to check the stats on how I compressed this. But I've had this problem before and KNOW that it was a completly different set of settings... i.e. one was MPEG and the other was MP4.
After awhile there is a pulsating feeling... seems to be just under a second in rythm, but for that split second the compression seems to get really bad... but litterally its a split second.
http://vimeo.com/3334424?pg=transcod...ed&sec=3334424 is a demo of the example... it doesnt start right away and I haven't watched just to notice when it does... but if you skip to about 11min 30seconds you can notice it.
Any clues?