According to the paint diagrams I have looked at in the PRRT&HS Journal (Pennsylvania RR Technical and HIstorical Society), the superstructures were all DGLE, almost black very dark green, as were steames. The frames and trucks were supposed to be painted black, not DGLE and this applied to both GEEPS and F-units. This is what the official RR instructions stated. What actually happened in different shops, we don't know for sure, but most locos probably got the company standard paint job.
I have noticed the differnece on models when I put a black one next to the a DGLE. When they stand alone, the DGLE usually looks black.
the other issues that arise are that weathering and dirt and sun beating down affected the perceived colors. I had a friend who insisted he remembered seeing dark blue pennsy diesels.