Ah! I see the problem here.. your pyramids are doubly-defined Several of your pyramids have the same geometry laying on top of itself twice. Also, ALL of your shapes are pyramids (4 sided), not diamonds (8 sided) - they have an overlapping inner wall that is not necessary.
In Netfabb, open your original file.
select the Repair tool
click the green cube on the toolbar - "Select Shells"
then select the outer tip of that middle point
- Observe that not all of the pyramid turns green even though it should.
click on the Delete button
You'll see that for the middle tip... you are deleting one side, and not the whole tip.
Your drawing program messed up, or you have two of the pyramids with identical geometry on top of each other.
The offending shape is like a piece of paper folded only once - there's no "thickness" to the wall - it looks okay to the eye, but since the thickness is 0, the automated programs are removing them.
I've PM'd you a version that doesn't have the issue, but you might want to go back to Maya and figure out if you actually have overlapping meshes, or if Maya is doing something wrong here. Unfortunately, I can't help you with Maya.