I know that this wont help you in your situation but I would always suggest not to use boolians unless its the only option available, or the mose plausable, say spliting an object or making a complex hole for an explosion, they seem like a great tool but they cause lots of problems getting them to work correctly (as in this case)
What I would do in this situation is to combine the mesh and then merge the verts, its a longer way round but you will have total control of where everything goes and therefore greater control over the topology, takes a bit of planning getting the verts to where you want them to be but its better in the long run.
I think further in the tutorial (on the legs) Kurt has a similar problem and uses the combine mesh method
"No pressure, no diamonds" Thomas Carlyle