I usually don't post much because I don't have the time to and I also tried to fix my problem on my own however I'm having a hard time figuring out what it could be... It might be related to my Color Profile but I don't really know for sure...
When I'm looking at my pictures in the Windows Photo Viewer they look exactly like what I'm seeing on my D800 screen which is perfect however when I open them with Lightroom 4.1 or Photoshop CS6 they doesn't look the same at all and I have to add a lot of Saturation and Vibrance to them. I took a screenshot to explain what I'm seeing...
The windows photo viewer is looking at the imbedded jpg which matches you in camera settings. ACR is working with the raw nef witch needs your input to process the photo.
You can try viewing the image using Windows photo viewer using the slideshow option (click the center button) and I think it will give you the result you want (ie it will match the other image). Viewing the image in the single image view mode never gives an accurate representation of the edited image. Waycool's post that the viewer is pulling the imbedded jpg might be correct. I've never had a good explanation to why it happens until now.