I just finished shooting for 5 days with the 5d mk2. We were using the magic lantern 'firmware' software on the camera. We shot on to a number of different CF cards: sandisk extrteme iii and extreme iv (8gb) as well as kingston 266x (8gb). On a few of the days (not everyday!) I got a lot of compression artifacts in the footage- it looks like some pixels get stuck for half a second around motion, such as you would see in a really badly compressed DVD or web video. This is on the footage straight out of the camera!
After the first time I noticed this, I re-formatted the cards using disk utility on my mac (even zero'd them out!), but it didn't help.
I can't seem to find anything on the internet about this issue, so I'm wondering if it is only this particular camera. We bought it just a few days before the shoot. Maybe it is defective and should be sent back?
As far as I can guess it is either:
-some problem with the formatting of the CF cards
-an issue with Magic Lantern software.