Since you are using the Rigid Transforms, the bodies will be attached to their respective axis. A joint is required to specify movement between the bodies and the reference frames. In order to create implement free-fall, you can insert a 6-DOF Joint block or a Planar Joint block to define the box's movement in relation to the environment. Port B of the block will be connected to the frame from where the body will be released and Port F will be connected to the body that will fall.
Using the 6-DOF will be the easiest to implement. If you decide to use the Prismatic Joint block, the Rigid Transforms will have rotate the frame for gravity to act on the box since the block uses the X-Y plane of the base frame as its constraint. The image below shows how to implement the 6-DOF Joint block.
Check out the following link on more information on 6-DOF Joint block: http://www.mathworks.com/help/physmod/sm/ref/6dofjoint.html
Check out the following link on more information on Planar Joint block: http://www.mathworks.com/help/physmod/sm/ref/planarjoint.html
