Not sure what is going on as when I tried it with cubes then all worked as expected. But when I imported a plant I get the issue - two of the three plants show up in the final render but none of the plants show in the ipr. I have tried changing the layers of the materials so they are on a visible layer but that doesnt help. I suppose the IPR and the final output should be identical anyway in terms of objects showing up so there is definitely something fishy.
Just a quick info about this issue. The issue is caused by having intances of an object, which is not visible itself. In normal cases, even C4D forbids this and makes the instances invisible. But in the case of invisible layers, somehow the instances can be visible. C4D circumvents the problem by a clever hack, that we think would cause more trouble because of the way our IR works now. We simply didn't expect invisible objects to be able to influence the rendered scene :-(
That said, I tried to fix this issue by a different clever hack, but it turns out that it does not work because of the fact that we are not able to synchronize layer information in IR. The bottom line is that the visibility issue is fixed, but the clever hack causes other issues and possibly instabilities that we don't want to push into the current Beta 1 version. This fix together with the layer synchronization will need some more time to implement and will appear in Beta 2.
Don't worry, you'll not have to wait for the final Beta 2 release, we will be doing daily builds as usual!