Hi Cindy - i always use spot metering and single focus point - the highlight blooming occurs ( naturally) in high contrast scenes. The spot metering allows me to shoot for highlights or shadows. I have just noticed that the D3 ( like the Canon) has less latitude than the DMR shooting similar scenes. This is anecdotal - I haven't experimented enough with the camera to find a workaround yet. The EV suggestion is worth trying. On the other hand, I have been positively delighted with how well the D3 works with flash - after the Canon 'system' it is a relief to be able to just shoot!
Hi There Peter
A couple of points - first of all, I'm certain that the D3 'over exposes' with relationship to other dSLR cameras. Cindy has a point with respect to the way the metering works, but even if you're using spot metering the same situation exists. It's of benefit in low light PJ type situations where you can almost always recover 'bright' bits, and the exposure means less noise in the shadow areas. But it isn't ideal for Nature.
If you go to the pencil menu, b6; fine tune optimal exposure, then you can dial in a value for each exposure type (I have 4/6 dialled in).
Secondly - like you, I've never used anything but spot metering . . . . but the matrix metering on the D3 is almost uncanny, and combined with the auto-iso features and this b6 fine tuning, I'm shooting very high contrast scenes, and I can count on the camera to get the exposure consistently right (actually, small white flower against hedge may need a little exposure compensation, but I've learned quickly where it'll be required).
So, my gut reaction is that your highlight blooming is NOT because the camera is inherently prone to blown highlights (I really think it isn't) but because it has a built in tendency for a higher exposure than other cameras (I can only assume that it's to keep detail in the shadows).