Can you determine if it is an aperture problem or not? Does the diaphragm open completely when you look into it on the camera, and close when set to a smaller aperture? What are the camera readings for the 100-400 vs. a known, good lens?
In manual mode once the light meter has been activated, I get different meter readings if the shutter putton is pushed halfway or not. It doesn't behave this way when using my 24-70. A meter reading is a meter reading regardless of what you do with the shutter button. Does this suggest anything about my problem?