Gary, as others have indicated, a high shutter speed is critical to freeze any wing flapping and you need a small enough aperture that you'll get some depth of focus. So shooting in manual is the way to go, especially if you're using auto ISO. (I have no idea what happens if you combine auto ISO with automated shutter priority.)
There have been some excellent threads is the past on BIF. Several were by Joe (in Florida if I recall correctly); his work is extremely good. Hopefully you can locate those threads.
Edit: after hunting, I found a number of the early BIF threads. This page contains a number of helpful comments by Joe:
Eagle in Flight - Help please