maybe this is a simple setting that I cannot find or is just something that doesn't happen on the d7000. a friend of mine (who shoots with a d3) and I were switching cameras and he noticed that on the d7000 the focus point doesn't stay illuminated between focus and capture. Is this something that can be easily modified?? I couldnt find it. When using his d3, the focus point stays illuminated very brightly (by comparison)until the image is captured.
Never used a D3, but the D7000 focus point only stayes on with AF-A and AF-C. With AF-S it illuminates until focus lock, then disappears.
To be honest, never noticed that till you posted this and I checked the way mine works.
So perhaps it just depended on focus mode set, even with the D3.
Edited to add:
Just realized I mostly shoot with single point. To test your issue I set the camera to auto-area to get it to act that way. Of course in single point mode, the selected focus point is always shown. Perhaps that's the difference.