the noise is due to the way the different codecs work; and probably also the way the camera is putting the image it into the 1920x720 frame..something like with what happens in extele mode. mjpeg is also only in 30fps. i have a 2x anamorphic and i rarely use the mjpeg modes. though i did find a patch that takes the hd mjpeg mode into 2k...so i need to test that out. the footage is still plenty usable. i shot this video with a 2x anamorphic and the canon fd 50mm/1.8. i was curious to see how the anamorphic fared handheld..(i'm still getting used to the dual focusing, there's some spots, most notably in the interview bits, where i was off..) https://vimeo.com/53870989
the only reason i'd use mjpeg is for the instant aspect ratio correction. and i can get ~2hrs of footage on my 64 gb card in mjpeg as opposed to just under 1hr in avchd/24p cinema mode (driftwood's canis majoris night or sedna patches). if you use the mjpeg mode, you don't need to do anything to the aspect ratio; it's correct and properly de-squeezed to use right off the card. for avchd footage that i shoot anamorphic, i interpret the footage and force the pixel size to anamorphic 2x.
and the only reason why it is in mjpeg mode is because you can't adjust the avchd dimensions like mjpeg. i'm guessing it has to do with the avchd codec being designed for hd formats, so it only works with the standard 1080/720 dimensions..but that's a complete guess. another advantage of mjpeg is that you can drop the frame rate down to 2fps for timelapse. i'm not sure if it would work to change the framerate to 24fps, without having issues. i haven't seen a patch with that, so i would assume it crashes.