You can only change the selected focus point when the meter is active, however the meter will switch off automatically when the review pops onto the screen, you can't change that.
Try this though; there is an option somewhere to have the meter activate when any button is pushed, not just the shutter release. As far as I can figure the meter should become active when you push the multi-directional pad to change the selected focus point if you enable this option, solving the problem. I'm using a D300 BTW but I'm pretty sure the option will be thee on the D3 too. I'm just looking through the menu for it now (can't remember what it's called), I'll post again if I find it.
Ah, I think I got a bit confused, there is an option to have pressing the multi-selector keep the meter active, but not actually activate it. Looks like you have just have to learn to live with the problem. All the best in finding a solution anyway.