UPDATE: read this blurb from the canonrumors posts (I don't know much about lens inner workings so I can't comment):
From the 5D Mark II Team site:
“Description of the problem:
When a Canon EF 100mm f/2.8 Macro USM lens is mounted on the camera and the user manually changes focus (rotates focus ring), the lens changes the iris/aperture â€œby itselfâ€, even when the camera is in full manual mode.
It is not normal, and should not happen. The tests were made by several users with many copies on many camera bodies, so itâ€™s not an isolated lens problem.
â–ª This malfunction always occurs in this situation:
When the camera is set to M (Manual) mode and in Live View mode (Still+Movie â€“ Movie Display), which is the correct mode for â€œfull manual controlâ€ in movie mode.”
Please read more of the details at the 5D Mark II Team page for this issue.
There is also good discussion over at canonrumors.
(Photo credit: snap from the video)