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...Doug, were you using IS for the 100-400 shots? If not then you have a problem with inadequate shutter speed.
For fast-moving subjects, IS isn't always enough. His BGs look reasonably steady, but the duck's head in the retriever shot, for example, is blurred while the dog isn't, and it was shot at 1/60. In the new group of images, the one of the duck making a water landing is sharp, and it was shot at 1/1600. The need for a faster SS is, I think, indicated in some of the shots.
...Did you also aim the lens correctly *before* activating the AF ? Otherwise it can try to track the wrong thing or nothing.
I think that was a big part of the problem. In the sample images, the ones that were in focus had a subject (or part of a subject in the case of large objects like dogs and people) right in the center of the frame, and in the ones that were OOF the subjects weren't centered.
BTW, not all shots came out bad but the keep ratio was very low.
The biggest problem in the flock-in-flight shots may be insufficient depth of field, in addition to missed focus target. With long lenses, f/8 gives a DoF that may not be deep enough to get all the ducks in the flock equally sharp.
Moving from 200 ISO to 400 or 800 could help all the noted problems except aim-point.