Canon makes great glass, but all of their lenses set the aperture electronically using the exposure system in the camera. That’s OK for single still photos, but when you’re doing multiple stills of a scene (we’re talking time lapse photography), you don’t want the metering system to make small variations. Even if you have manually set all the exposure controls on the camera, apparently the physical tolerances of modern cameras will not allow them to open the iris blades to EXACTLY the same degree for each exposure. That small variation will look like flicker when you play the images back as video.
New Planet5D writer Dustin Farrell has a lot of experience doing time lapse (check out his video – amazing!) and shows us a hack to physically lock the iris blades and avoid the camera adjusting iris between exposures.