Are you comparing Apples to Apples? The D90w/18-105mm is listed at $1099.00 and the D7000w/18-105mm is listed at $1396.95 after a $100.00 rebate. There is a similar difference in price between D90 Body Only ($849.00) and D7000 Body Only ($1096.95 after a $100.00 rebate. About a$300.00 difference w/ lens and about a $250.00 difference body only both after rebates.
Trying to figure out pricing policies will lead to madness. The last few times I checked prices at the Nikon Store, Refurbished D3's were priced significantly higher than Refurbished D3s's. Given how much better the D3s is, I am mystified at the difference in price. Good Luck and Enjoy your Nikons!