I found the old 5D2 to very problematic with focus unlike the old 5D which just seemed to nail it time and time again - static subjects that is.
Something is wrong with your Mark II. The two 5D's have the same focus system and should behave exactly the same.
My 5D Mark II did reveal that some of my lenses weren't working as well as they should have been, thanks to the extra resolution.
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