If I remember correctly - during my first month or two with the D40 I shot in JPEG, 3D Matrix Metering and sRGB III - just loved the enhanced blues and greens in sRGB III
- but the associated tone curve was a bit too contrasty and clipped the highlights in some cases. At that time I did use a -0.3 exposure compensation when shooting in bright light...
You also need to be careful with Nikon's 3d Matrix Metering - although it's supposed to consider the entire frame equally, it does give a bit of priority to the area containing the active focus sensor - not as much as on the D80... from what I've read. The center weighted average and spot metering modes conform to everybody's common understanding of what they should do. So, I wouldn't say it's a bug... it's a feature! LOL
Just make sure you use the appropriate metering mode for your shot.
For me it wasn't such a big issue because I used -0.3 and sometimes even -0.7 on the P&S cameras I owned before the D40.
When Adobe updated ACR to read D40 NEFs I switched to RAW and reset the EC to 0.0. with NEFs I seldom have to compensate my pictures with more than +/- 0.5 in PP (like one in a hundred).