Dick, I direct your attention to the photo on page 78 of Morning
Sun's "Rock Island in Color Volume 1"... PFE 47036, which otherwise
has an ordinary dual b/w heralds paint scheme, definitely appears
(at least to me) to have black ends. The photo date is 1961 and the
car has a few years of weathering. It's possible that metallic red
paint morphed into a uniformly dark shade that starkly contrasts
with the car roof but.... I've long been intrigued by this photo.
In fact there are five PFE reefers in the shot, but only the 47036
shows an extremely dark end.

I do agree with you, I don't know of any black roofs in this era.
Unfortunately many vendors have painted PFE cars with black ends
and black roofs and that has created an impression on modelers
that is hard to fix.

Tim O'Connor