First: Ducky you did really great work. The speed up, I get by using your combiner is incredible. THANK YOU!
Back to my problem:
I already compared the mesh-material of the original to that of the combined one and found no difference.
Now I have a guess, but no solution:
I create the cubes out of single planes for each different side. When I used cubes, I had problems with the visibility of the cubes after combining (see picture).
If I look from the oppsite direction to my mesh, everythink looks ok, but the lighting seems to be different from the original as well.
It's not too easy to give my mesh to you, because it is generated on the fly. So I have no file to share. I could only save the whole scene.