Repro steps:
1) Open the project and run box scene
2) Bake the lights and notice that the transparent box is very dark inside
3) Also, notice that the front of Transparent box is not red, even though it should be
4) Try disabling the Transparent object and rebuilding lights and you will see the front becoming red again

Workaround: Move the transparent object slightly to front - it will restore the red color to object, but won't change the dark lighting inside the box