Lightmap UVs squashed in atlas

Upgrading the project unity 4.6 to 5.1, I noticed some differences in the lightmap. Unity 5.1 seems to have softer shadows on lights than in 4.6, the directional light casting these shadows both have 0.35 shadow angle.

However they also seem to be lower res, because of a strange squashing seen in the lightmap atlas.
On the attached image you can see the 4.6 atlas on the left. The area marked is the ground, it matches proportions to how the groundplane actually is in the level. On the right you see the unity 5.1 lightmap atlas, which seems to be squashed together for some reason.

Ideas? Mesh's lightmapper uvs created by unity in both cases. Same resolution and padding, both bakes resulted in 6x1024 lightmaps.

 

On other areas of the same ground, the difference in the lightmap is also quite big. This is a shadow cast from a hard shadow light. (Baked shadow radius = 0)

Unity 4.6 on the left, Unity 5.1 on the right

 

I'm afraid that this has already been posted here: http://forum.unity3d.com/threads/lightmap-uvs-stretched.313379/#post-2067538 but the official answer is that the UVs are not stretched... I have tried to explain that indeed they are but without luck.

 

Checked out your thread, seems to be the same issue. UVs are squashed (or stretched, but I'm leaning towards squashed ) and the resulting free space goes unused. It's almost like it finds a spot for the actual UV island to fit. Then it scales the whole UV square layout down to fit into the appropriate area. Instead of only placing that specific UV island unscaled there. If that makes sense.

I can move my squashed UV problem over to your post if you like.

 

Whatever you prefer

There are even more problems related to UV and lightmapping. As an example if you make your custom lightmap UV layout from max/maya etc and you don't fill ALL the uv space, this free space is not used by the Unity's uv packing for any other object of the scene.

 

And do the ones that don't use all the space get squashed? Sounds like a plausible bug in a packer.
1. Checks size of uv island, ignoring empty space as it should. Finds an empty spot.
2. Fits whole uv layout into available space, forgets to take empty space into consideration.