Flickering typically happens for three main reasons:
1) You aren't using full manual controls on your camera (unlikely)
2) You are using HDR processing software which makes adjustments based on the contents of each frame
3) The iris on your lens isn't stopping down to the same amount for each frame (likely)
You may have noticed that you aren't having any flickering problems with the Samyang lens. This is because the iris on this lens is fixed when you set it to a given f-stop. To cure the problem on your Canon lenses, do the following:
1) Set the f-stop in the camera that you want
2) Press the depth of field preview button to stop the lens down
3) While holding this DOF button down, press the lens release button and rotate the lens slightly so that electronic contact is removed between the camera and the lens. However the lens should still be securely mounted to the camera.
Voila! Your aperture is now fixed and you won't have flickering problems.