The box symbol and the box with a dot symbol are both signs of under-constrained parts. This does not mean that they are not contstrained to your requirements, just that parts can be moved with the "drag components" command. The box symbol means that there is at least 1 degree of freedom (DoF) unconstrained, and the box with a dot means there is a child object attached to the object with the unconstrained DoF.
For example: I am assembling an electrical box. The box body is locked to the X,Y, and Z planes and has 0 unconstrained DoF. If I attach a hinge, the first half of the hinge is fixed X, Y, and Z to the box body, but the second half of the hinge might be set up with a pin connection. This part would start with a box icon next to the part in the model tree because it can still rotate. If I then attached a door to the second half of the hinge, even though the door is locked X, Y, and Z to the second hinge part, the second hinge part is not fully locked. At this point, the second hinge have woudl have a box with a dot and the door would have a box next to their icons in the model tree.
The way I work around this (with hinged enclosures, anyway) is to define a plane through the axis of rotation with an angular offest. Then I constrain my rotational component's lateral motion and insert (I am still on WF4) the two circular surfaces. Finally, I constrain the rotation by using the new plane I created. In this way, I am always fully constrained, but I can define my rotation based on the angle of my plane.
