TMG1961 - Try switching off A5 - (Note - this will stop the focus point when you do use the back button also, so it may be hard to focus if you use single point) I believe BeegRhob nailed it, I think it is the exposure meter triggering it and its just showing where the "focus" point is in regard to the frame. Even more possibly confusing if you "recompose" (one reason to use BBF) and do a half press for exposure the light will not be on the "original" (when you first hit the back button to focus) point at all.
I have gotten used to it, I think you can as well once you know whats going on. I only worry where the box is when I "am" focusing using the back button, I ignore it any other time.
Give yourself a while to get used to back button focus, it has taken quite a while for me to "stay" with it. For me I needed to have some other settings a certain way to have maximum success with BBF.
All the best