Mike and Tim,
Great picture! It's amazing what shows up on eBay.
It's probably safe to say that the C&S cars were spray painted. This was a common practice back then and I have pictures showing AT&SF cars being sprayed in the 1930's. The compressor and paint pot were on the ground and the painter held a 6 - 8' long wand with a spray tip. This allowed them to reach up high as well as underneath the cars.
To state the obvious, we have to take these pictures for what they are - a snapshot in time. For all we know, the car could have been painted pink the day, week, month, 5 years before the picture was snapped. When we assume that things were "always" a certain way, based on one picture, we get in trouble.
My guess follows Mike's thinking that the roofs were originally painted the car color. Then possibly sometime later, as the roof developed leaks or whatever, it could have had a fresh layer of roofing tar or tar paper applied. Then based on variables such as availability of paint or the foreman's instructions, the roof may or may not have been repainted. The world will never know for sure.
Thanks!
Doug
Doug Heitkamp
Centennial, CO