Meanwhile, back on topic, I have done some more controlled experiments this morning.
Conclusion:
It's the 5DMkII in portrait mode.
My 5D does not show this, my 1D3 does not show this, and I have tried 24-70 f2.8L, 70-200 f2.8L and 50mm f1.4 lenses. All show the same internal reflection, regardless of filter or hood.
Here's what I did:
This is my overall scene - basically a reasonably dark-ish subject, but with a bright object outside the field of view of the lens. Here's the scene zoomed back a bit:
Next, I mounted my 70-200 f2.8L, with filter and hood, onto a tripod, at 70mm I can only see the wall section, not the window.
5D2 image:
then just changing the camera to the 5D and altering nothing else:
Settings being ISO 100, f2.8, 1/40th @ 70mm
For verification, I put on the 50mm f1.4 lens, no filter, no hood, handheld:
5D2:

5D:
Looking closesely at the way the reflection is curved on it's left side, I suspect that if the hood was a bit longer it would not happen...BUT.. these reflections do not occur on the 5D.
Also, these reflections only occur when the mirror is up, they are not detectable through the viewfinder - which is a major problem as you don't know they have happened until you review the images (or use live-view).
These reflections do not occur in landscape mode, only in portrait mode.
So, why the difference between the 5D and the 5D2 ?
I am going to have to be very much more aware of what is outside my field of view when using the 5D with any lens now. Or is it a fault with my 5D2?
Comments...?