Ok, I've found the issue. For the short term, try this for a solution:
in = inpolyhedron(myStl,X + 0.0001);
The reason you were having issues is that the faces/vertices you have are exactly aligned with the grid of your query points. This means that every query point lies exactly ON an edge. At the moment in my code, ON is considered OUT of the surface (only IN is considered IN). I had only anticipated this would be an issue for the outer surface points, but the same issue arises for inner points too like in your case.
In the help file I mention this as an issue awaiting user feedback. It looks like you're giving that feedback - thanks.
For the moment, just use the little work-around I gave. I think from your example I will try to change the definition so that I add a small tolerance to regard ON query points as actually IN to address this issue in a next version of inpolyhedron.
@Nick and Adam, I'm not sure what issues may be at play with your files. Feel free to email a .mat file with your points/faces data *and* the 2 or 3 lines you use to create a working(!) figure from this data in MATLAB (note that I'll only have time to look at it if the figure creates cleanly).