This is how I cut box joints for my hive bodies using a router with a pattern bit (Freud bit number 50-102 purchased on Amazon) and a box joint pattern as shown in the July/August 2012 issue of ShopNotes magazine. I made the pattern long enough to cut box joints for supers on one end and brood boxes on the other end which I made the fingers different sizes. It works great and I did not need to make any adjustments. One advantage is that lumber that is slightly cupped can be flattened with a a clamp and then the box joint cut.

http://s1294.photobucket.com/user/salesi24916/library/