Intersection Vs Penetration ?

Hello,

I couldn't distinguish between intersection and penetration. In the model (image in the link below), i could see the penetration of elements, still the penetration check tool shows no penetration, only intersections.

My doubt is whether penetration is checked only with certain normal angle?

https://drive.google.com/file/d/0B2rIYPnVjYNESWxNcVdveExXSW8/view?usp=sharing

Ahilan