Hello, folks. Here are the results of two hours of banging-head-on-keyboard troubleshooting, distilled down to a dozen easy steps:
1. Create some particles.
2. Create some geometry.
3. Instance geometry to particles.
4. Render: looks fine!
5. Create a new layer.
6. Make it a reference layer.
7. Add the particle object to the reference layer.
8. Render: looks fine!
9. Add the geometry object to the reference layer.
10. Render: looks fine!
11. Add the instancer node to the reference layer.
12. Render: WRONG! Instanced geometry does not appear in the render!!
I am sure this is not intended behaviour. Can anyone confirm this in Maya 7, 8, 8.5? If so I'll holler at Autodesk.
...the steps of adding the particles and the geometry to the reference layer are not necessary. I just included them to show that it is the instancer node which is the culprit, since nothing else seems to mind being on a reference layer.