Whenever I have a piece of simple geometry such as a box, or multiple boxes, if they are a primitive mesh and not a polygon and I make them a RBD glue or fracture object, each face will become an object, instead of each box becoming an object. How do I make it so each box is an object in the RBD simulation, instead of each face.

Have you done something that made the points unique? Perhaps try a Fuse sop and see if the results are any better? Would you be able to post a hip file? I've tried a lot of different combinations and have not observed anything out of the ordinary?