Have you tried playing around with different focusing and tracking settings? From experience with teh 7D, which has a less complex system, when the subject is small in the frame, spot focus often gives better results. If you add in the different tracking scenarios, then you may need to experiment to get the best out of the focus system on the 5D MkIII. What works wiht the 24-105 may not work with the 100-400, because the scenario may be different (at the very least, the subject will be further away). Also bear in mind, that with a longer telephoto, you are compressing the atmosphere between camera and subject, so you will get greater problems with pollution affecting image quality. I spent quite some time trying to understand why some days, I just couldn't get a sharp shot with my 7D and 300 f/2.8+1.4x extender, when other days the combination was sharp. It turned out it was due to the compression of heat haze and moisture, as on each occasion, the subject was low to the ground and there had been mist earlier in the day.