D90 Picture Controls and Lightroom, help needed

I took some shots with a rented 300 f/4 AF-S and my D90. I usually shoot RAW+JPEG basic, use the RAW shots for images I really like and want to edit, and then keep a few Jpg's that I don't care to edit but want to keep anyway.

I have been using Lightroom 3 for a few days, and have noticed that most of my shots after I've adjusted the WB to my liking when I hit "AUTO TONE" it gives me LESS brightness and a lot MORE contrast, and generally made my shots look a lot better. My shots just looked too washed out, but were in good focus and not overexposed, and the auto tone feature fixed this. I then made my fine adjustments on some shots, but the auto tone was pretty accurate with these shots.

I would like to know if this has to do with the Picture control settings that I am using? I have the Auto D LIGHTING set to auto, so contrast cannot be adjusted. I was under the impression that the picture controls were just for jpgs and wouldn't effect the RAW images that I see in Lightroom. Someone please set me straight. Am I looking at a RAW image in LR and would my Picture controls make my shots appear less contrasty if I have them wrong? Thank you!