First I thought you haven't updated CS4 to get all the properties for RAW images. But you did. And if that doesn't work in Element and Lightroom I'm at a loss too. You can send one of your NEF file to me, either in private message or email, and I can try here so just to see whether it's your file or software.
Nikon D90, D80
Nikkor 16-85mm AF-S DX F/3.5-5.6G ED VR, Tamron SP AF 28-75mm F/2.8 XR Di LD Aspherical (IF) macro, Nikkor 50mm F/1.4D, Nikkor 50mm F/1.8D, Nikkor AF-S VR 70-300mm F/4.5-5.6G IF-ED, Sigma 105mm F/2.8 EX DG Macro ||| 2x SB800 | SB600 ||| Manfrotto 190XB