I would be interested in two things. 1) What software do you use for editing the pictures. 2) How do you use D-lighting
If I have understood it right the camera does underexpose when you use D-lighting, the more contrast rich scene the more underexposure. That's because you don't want to clip the highlights. Then the software boosts (lift up) the dark areas.
I suggest following: Test taking a picture with harsh light. Use aperture mode. Test with different set-up with D-lighting and see how the camera reacts. Different shutter speeds I will guess. I have not done this myself yet, but I think I will test it.
If you use Nikons software it may handle this better than other programs that doesn't read the complete setup in the NEF-file, neglcting your Expeed 2 settings...
/Mikael ----------------------- D800 & D7000 user (Sweden)