Algodoo

You made the same mistake that many non-chess players make. That is, you set up the board with the darker square in the lower-right corner. That should be the lighter square. It's the only way that the queen can start out on her own color with the pieces set up correctly. So, you need to rotate the board by 90 degrees (in either direction) and then set up the board correctly. Do a Google search for some examples of properly setting up a chessboard.

It's always good to make sure that your scenes are accurate before posting them!