Most of the regulars here are primarily stills shooters, so video questions don't seem to generate a lot of discussion. There is a video-specific area in the forums at CanonRumors.com, I suggest posting up there if nobody here has any ideas. I don't shoot video at all, so I don't know much about it, but I thought most 'serious' video shooters shoot manual focus, no?
It is difficult to ascertain from your post what may be causing this issue. If you are shooting with an Image Stabilized lens, ensure that you have deactivated the Image Stabilization on the lens as this could cause the image to be shaky.
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