before you do any kind of boolean, make sure that you have only TWO operands. if you want to subtract many objects from one, perform a 'combine' (polygons-->combine) before you do the boolean. that helps ensure that you're subtracting one object from another. multiple objects just complicates things.

for example, say you have 7 cylinders you want to subtract from a cube. instead of doing 7 boolean subtracts, combine the 7 cylinders into one poly object (even though they're not all one object), delete your history on the newly made object, and THEN do your boolean. it should work.