Okay, I'm still what most would call a "newbie". Can you explain "backfocus", or is there a website where I can read about it? Another thing is that I am at maximum zoom, if that makes a difference. I can use the same lens from the same position and shoot closer objects, and the problem does not occur, or it is minimized.
The Depth of Field (DOF) at 200 feet using the 2x extender at wide open aperture (F5.6) at maximum zoom is about 2 feet. That is the range around the focus point that will be considered sharp in the image. Anything outside that will be blurry. See http://www.photozone.de/3Technology/demos/depth.htm
for more info and a calculator. Anyways, that is sufficient DOF that my comment about leaning forward or back doesn't apply. You cannot cover 2 feet by just leaning I think :-)
Backfocus means that the camera plus lens combination think they focussed at a certain point, but in fact the real focus is behind that point. Front-focus is the opposite effect. But since you say the problem goes away when you focus closer objects, my guess is there's no backfocus problem. Also, closer objects (at the same zoom and aperture) mean a narrower DOF, thus if you had such a problem it would be more pronounced....
That makes me think of possibly three things:
1. The AF sensor is actually larger than the square in your viewfinder. That could mean the AF sensor can pick up, and focus, on objects behind what you are trying to focus on. This can happen if the square in the viewfinder is on the edge of the object you want to focus on. See this picture (which I kindly borrowed from NHL, thanks!)
2. You accidently touched the manual focus ring (I've done that by holding the lens in the palm of my hand and my finger just touched it and changed it a little)
3. You focussed by pressing the shutter half way, then zoomed in.
Anyways, some suggestions to look at. Hope you'll figure it out!