I really notice the contrast loss when I compare photos side by side. This past trip I took to the Tetons, I photographed some bison with the TC and then removed it as the light was fading. The shots with the 70-200 alone are leagues better. I'll see if I can post a couple examples when I get home from work.
What settings did you change on the D800? I always shoot RAW but I don't think any camera settings really impact photos aside from the basic exposure values (shutter speed, f-stop, ISO, maybe ADL and in camera noise reduction). If you're shooting JPEG, then all those Nikon settings and color controls can really impact output.