Originally Posted by Fritzvds
I was acctually standing on the shore not a boat (you would be suprised how close these animals come in

)
My mistake. Still, like I said, you were kind of borderline - at that shutter speed and focal length, you have a right to expect more than 50% of your shots to be sharp, but not all. And the ones that won't be are the ones where you were kind of hurrying rather than taking your time to carefully brace yourself.
Throw in the other factors - the fact that the camera may well have chosen to focus on the horizon rather than whale, the diffraction from the way-too-high aperture, the quality of the air itself - and as you say, there were indeed quite a few factors contributing to this shot coming out the way it did.
The only thing I could think that would maybe effecting it is the blue sky and blue water making it hard for the autofocus
It's not the fact that they are blue. It's the fact that by far the "easiest" target for a AF system is a clear line between a dark object and a light object. And the nice, long, straight, non-moving, horizontal border between the dark water and light sky is just *begging* the AF system to focus there, not on the little dark non-descript shape that popped into view for a fraction of a second. There's basically no reason in the world to expect the AF system to have found the whale when the horizon made a much easier target.