The big box method (whether it's textured with sky or not) is just a very bad way to fix leaks. Unnecessary high amounts of faces (those on the outside of the level and inside of the large box) have to be compiled then, wich is just senseless extra work. Find the leak and fix it good.
Either your box was an entity or you had an entity outside the box.
Find the leak? Have you tried the pointfile method already?