I just completed an HDV project that had the very problem.
The client was logging footage and wanted clips right at
the exact moment there was a scene change which caused
the batch capture to fail on about 15% of the clips.
My workaround for this is:
tell your camera people to roll for at least 10 seconds
before action, and keep it rolling at least 10 seconds after
the action is done.
Tell the person logging footage for later capture that
they can only log after the first 10 seconds of a scene
change and 10 seconds before the next scene.
Though if they look at the footage if the shooter did
it properly, it should be obvious.