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I'm having the same issues with my 100-500, no teleconverter, the AF is terrible now, both single point and eye AF. All since the update 

I've just updated from 1.7.1 to 1.9.0 and am having the exact same issue with the exact same setup (except my 500mm is the latest one, not the first version). Animal eye AF has just lost the plot now! I photographed a squirrel from super close range,...