Same problem
 

Alon, I'm wondering if you've discovered any solution to the flickering problem. I'm having the same problem... all manual, shooting primarily with an 85mm 1.2... static interviews, low light situations. ISO is locked, shutter is locked, WB is locked. It's just as you described, a slight flicker, especially in the darker areas of the shot... driving me nuts.

I'm seeing exactly the same problem. Slight exposure shifts with everything otherwise on manual. Has anyone gotten to the bottom of this, and is it clear the firmware update fixes it? I'm on a shoot in the Amazon, about 24 hours from being off-grid completely, and would love to know if there's a fix.

2.0.7 doesn't fix this issue. I have a new 5D Mark II with 2.0.7 and using a Fotodiox adapter with the AF confirmation dandelion. As noted in the link to the discussion on Flickr, I see the aperture occasionally bump to 00 from it's normal state of 1.4 and I get a change in exposure along with that. Fotodiox was not sure what it could be either and asked me to send back the adapter and order a new one so they could see if their product was at fault. I suspect it isn't now though based on the frequency of this problem regardless of the brand of adapter. My guess is a software bug but I'm willing to bet Canon won't waste a lot of cycles on running it down if their lenses are working just fine.

Ditto, I have exactly the same problem, especially noticeable during locked down interviews.

Don't have a 5d but with my 550d I also see this occasionally in certain lighting conditions (also in darker area's of the image), looks like the flicker you get when filming an lcd screen with the wrong shutter speed, when I then lower my shutter to 1/30 the flicker almost completely disappears, if I choose a higher shutter it gets much more visible. Have not been able to get rid of it completely when it occurs. If I film that exact same scene with my main cam, a xh-a1 I don't have that problem.