When my wife and I were writing books on cameras, we noticed while testing the cameras, the menu system would not work as it would be expected. We suspect that by using oddball combination of commands or by careless handling of the camera (removing the battery without turning it off) we had "confused" its CPU. Many of the cameras we had tested allowed the body to be initialized to its default settings. This frequently resulted in a loss of our custom settings and the time/area setting of our camera. I know the a77 camera has an initialize command in its Setup menu. Might the a99 have a similar setting?
If so, you might try an "initialize" command to see if you can get the 70-200 mm to work consistently.