RJ, you are correct about bricks with no wood (smoke won't affect your autotune). You want to make sure the smoker is setup as close to "actual" cooking conditions as possible. When I autotune, I foil the bottom and lid of the smoke box, and poke a hole in the drain hole, just like for cooking. Add a water pan next to the smoke box, and 2-3 bricks (not foil-wrapped or anything) on a shelf as high as possible.
If you set the autotune parameter as you have, and enter the program at the time of the autotune (don't use a "stored" program, you should get an accurate tune. If it's not stabilizing closer than 5°, you may want to repeat the tune.