There are a number of things that can cause the disappearing geometry...

1. The surfaces must completely intersect

2. The surface normals must match direction. You can test this by turning off two-sided lighting (its under the lighting menu)

3. The geometry must by manifold. You can check for and correct bad geometry by running the clean up under the mesh options.

Those are the main things to check. Also run a test by creating two poly cylinders and just scale one down and then make sure boolean works on them.