Baked LightMap issues

This is an interesting combination of issues I have found here.

Until before this point I haven't used baked lights and lived with the strange lighting effects you get if you reach your pixel light count limit.

But that was annoying, so today I set my current scene up for baking lightmaps. All meshed objects imported were set to "Generate Lightmap UVs", lights were set to Baked mode. I went to the Lighting tab and created my lightmaps.

The first issue came up and it seams to relate to my terrain. I get this error if I bake the lightmap with my terrain enabled:

 Assertion failed on expression: 'terrainInstanceHashes.find (instances[i].instanceID) != terrainInstanceHashes.end ()'

I cancelled the baking, disabled the terrain to see if the lightmaps are created properly and discovered the second error I get:

 Assertion failed on expression: 'si.atlasOffsetX > systemInfo.atlasOffsetX || si.atlasOffsetY > systemInfo.atlasOffsetY'

If I go and bake the lightmaps now, the procedure doesn't take much time but interestingly gives me the first error seven and the second one three times. And there are two more strange things happening here:

1. Every map generated for global illuination is equal in objects shown, except for the Directionality one, I guess that the error originates here:

2. The problem with the rest of these maps is, that most of the objects are ignored in the baking process, here is how the scene looks like in shaded mode: The whole cathedral for example is ignored completely. It contains the lights that are the reason for baking the lights, standing in the cathedral now means: No lights anywhere except for the realtime moonlight.

It would be really interesting to find out what is causing these issues because that is really frustrating. Thanks for all answers, Manu