Here's a Key to making precise Box Joint Cuts.

I believe that all jigs share the same principle in that they work or use a key and spacing system and in order to have a smooth joint the spacing has to be precise any minute fluctuation in the spacing can leave for a bad joint, 1. A gap between each pin (box joint) and slot is caused by a key (spacing) that’s too close to the bit meaning when first setting up for the cut depending on the size of your joints when spacing between the bit and the guide pin or guide bar the spacing was to close between the two, 2. If the pins (box joint) won’t fit in the slots at all, the key was setup too far away from the router bit when spacing between the guide pin or guide bar, 3. If you have an offset from the top and bottom of the box sides this is caused by not having the work piece fully seated against the key before making the cut.