Sometimes the first mesh added to a scene will look incorrect in Shaded view during PLM bake, until the final stage completes.
The lightmap texture looks correct in visualization mode 'Baked Lightmap', so the lightmap itself is not incorrect.
Switching off Directional Mode in Lightmapping Settings makes the mesh look correct during bake.
Sometimes, duplicating the mesh and hiding the old one makes the new mesh display correctly during bake.
Switching lightmapping backend to enlighten and back sometimes returns the incorrect behavior.

It could be that there is an issue with some of the graphic buffers being assigned, or their index (since switching off directionality updates the object maps)

1. Download and open the attached project 'enlighten pvr intensity mismatch - 2017.3'
2. Open the scene 'point light corner'
3. Switch the backend to Progressive and let autobake run
4. Observe the floor plane does not look correct during bake
5. Set Directional mode to Non-Directional
6. Observe the floor plane now looks correct during autobake