MacOS Sierra Version 10.12.1
Graphics Card - Intel HD Graphics 6000 1536 MB
Blender Version 2.72a
When I open my STL file there are faces that appear and disappear as I rotate in the file.
I am not sure why the face are missing but I have done a lot of complex work on it and I'm sure there was something I didn't know do right.
I used the j key to join vertices a lot and the merge tool to merge many vertices.
Based on a (as simple as possible) attached .blend file with minimum amount of steps
Blender File -
STL File -