When in the third Third-person mode (the one where you can fly around independently of your ship), the targetting box is not updated. Witness these screenshots, taken within seconds of each other:

http://www.roguelazer.com/Bugs/targetboxbug.jpg
http://www.roguelazer.com/Bugs/targetboxbug2.jpg

It seems that the position code for the target box is based off of the ship position, not the viewpoint position. The probably means that in mouselook mode, the target box gets a little bit off. I haven't tested that yet.

I noticed the same thing, but didn't know how to explain it...