I am having problems seeing up different scenes.
Even a full copy of a scene that renders fine on the original scene returns:
Error: Scene parsing error: Error while binding material 'WhiteOak.dark.blend' to geometry 'Base1.001': No such material defined 'WhiteOak.dark.blend'
when I try to render the second, full copy, of that scene. On other occasions when "linking objet data" the export also goes fine and indigo just crashes right after start. I'll keep investigating.
Blender 2.6.1, Blendigo 3.2.6, Indigo 3.2.9.
Also the "glass acceleration" setting in Blender does not seem to transfer over to Indigo (or at least it's not "checked" in the Indigo UI. I have not verified by actually checking Blendigo's output.
Edit:
My BAD! Full copy should work. I forgot to reassign textures etc.

However, when adding a new scene with "link object data" Indigo still crashes.
Edit 2:
Sometimes the only thing that helps is appending the whole shebang piece by piece into a new Blender file. Somehow in the "old" file Blender retains data on objects/meshes that one thinks is already deleted. E.g. I had assigned a clay material to a mesh initially but later I deleted it. It also does not show up in the materials list anymore. However on export Indigo still complained about that material not being defined.
Again, I moved all the bits & pieces into a new Blender file by opening a new file and appending the parts of the objects from the old file that I wanted. That seems to clean out old data..