The joint component must be residing inside/under the timber component. Have a look in the Outliner-window, there you se a hierarchical tree, and the joint component must be in the level underneath the timber component, for you to be able to assign it as a Joint.
Actually, the joint will work perfectly even though it is not connected to the timber it belongs to, as long as it´s cut plane sits snugly to the rieceving timber's face.

Have a look at the movie "Creating a joint from scratch" at http://www.northernlightstimberframing.com/su/