Reflection Probe Missing in Flight
The VAB/SPH use a static cubemap for the new shader, but there is no cubemap during flight, thus causing any part being 100% reflective to be black and any partial reflective to blend with black.
I've created a quick, albeit inaccurate fix for this on my own:
1. During GameEvents.onVesselCreate, I add a reflection probe to the vessel gameObject if one does not exist.
2. The reflection probe is set to real-time, individual-faces, and appropriate cullingMask
While my 'fix' may not be ideal, it at least allows the lighting on the parts that use the new shader to be better.
You can see example screenshots here (the Kerbal is set to be 100% reflective):