Matt,
When you combine two hives and the desirable queen is in the upper hive, all
of the bees (both the foragers in the lower hive as well as the upper hive)
GO THROUGH the bottom to get to the entrance and these "strange" new bees
cause a disturbance
within the bottom hive, causing the bees in the bottom hive to "put the
blame" on their queen.  Meanwhile all is quiet and serene up in the top box
and the queen there is well protected by the gathering of her nurse bees
around her hive.  It boils down to a difference in bee moral between the two
hives.  The bottom hive is upset by the
infusion of top hive bees passing through to get to the bottom entrance; but
meanwhile, nothing is disturbing the moral in the upper hive.

I hope I have helped.

George Imirie