You need to make sure that every little bit that goes to make up the object has a boolean property assigned to it.  For instance if you use a sphere to cut out part of a cylinder and then grouped those two together - that resulting group also needs to have a boolean property assigned to it - in other words don't leave anything at 'Neutral', no cube, or sphere - or group.

So if you have used primitives, and/or terrains, or lattices to intersect, cut out or join - and grouped those primitives at each separate operation - then each of those primitives - and their groups need to be changed from Neutral in order for the accumulation of boolean operations to have all worked & to include everything in the final object.

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