Perhaps you've applied the uniform/non-uniform scale (or whatever it's called) and forgot to apply reset X-form?
Not that I remember.
It's actually only a squeezed sphere, with some edges moved.
Additionally I cannot reproduce this bug with any other object (simple spheres work just fine, so do more complex structures) until now.
I tried another thing:
1. Exporting the correct model.
2. Importing it again, of course with the previously described bug.
3. Scaling the model to its original size (actually only it's only squeezed along the z-axis).
4. Exporting the rescaled model.
5. Reimporting the rescaled model.
6. Result:
[ external image ]
Scaled along the z-axis again, but in the other direction.

Maybe this helps finding the problem.
Greets,
ScRaT
EDIT: Found the problem. As you said, I didn't apply Reset XForm (I didn't even knew it existed, plus it is not a modifier, but a utility).
Now everything works just fine!
Thanks for this great script!