Me autocontesto:
If the ShapeInstanceTime attribute is defined, then the instances are done through mental ray assemblies (for mental ray only, of course). Unfortunately, these don’t get called during the lightmap generation stage, since they’d all have to be loaded in, and so the SSS lightmap doesn’t cover them.
If you remove the ShapeInstanceTime atttribute from the graph, it should work as expected. The “Set Instance Geometry” sets this attribute implicitly, so use the “Instance Shape” node directly instead.
It’s an unfortunate limitation that we’ll have to live with for now.