Your comments

The issue is that the lightmapper won't bake shaders with cutoff. They will however bake with alpha blend. I do believe this to be a Unity issue.
Temporary, possible, fix!
1. Change all shaders to Forward.
2. Reassign all OpacityClip to Opacity.
3. Bake lightMaps.
4. Reassign all Opacty back to OpacityClip
5. Change all shaders back to Differed.
Bam! Lightmaps for clipped Differed objects.
PBL with Unity5 and a reflection probe works quite well for me.
You should come check us out. We are going to be at GDC and we use SF for just about everything. Good Mood Creators booth number PL100.
We are going to be showing our game at various shows in the near future and would greatly benefit from the performance increase of lightmapping. Any eta on a fix for 4.6?
I tried in SF 1.04 and the problem still persists and Unity 4.6.b20. I'll try with beta5 later tonight.
More specifically it is 4.6.0b20
Currently 4 but we will be switching to 5 at some point.
Deferred lightmapping breaks when I have a Texture2D in the Specular nodes.