Since some time I'm noticing flickering issue in certain clip from my canon cameras (booth 5d3 and 5d2) I've discovered that this is caused by a slight variation of diaphragm aperture. You can clearly see the iris slightly open an close throw the front glass. That happens when the camera is set to "1/3 EV steps", only using intermediary apertures; so 2.8, 4, 5.6, 8, 11 are stable, while 3.2, 3.5, 4.5, 5.0 etc flikers. Setting the camera to "1/2 EV steps" all apertures work fine. That happens both with 5d3 and 5d2 (no matter which built), but only with two of my canon lenses: 24-70 2.8 II and 100mm 2.8 IS macro, while the 24-70 mk1, 50 1.4, 16-35 2.8 mk1 and 70-200 IS 2.8 mk1 work fine.
Today I finally discovered that the issue is caused by Magic Lantern and in particular by "Exposure Override" option se to on. It is enough to switch it off to see the problem disappear.
I just wanted to share that.