Contrary to what a lot of builders' photos would have us believe, the PM did not specify black doors on its boxcars. The doors were only painted that way in builders' photos to show off the details of the door as distinct from the sides of the car. In the several hundred PM freight car photos I've seen over the years, I've never seen a photo of one in revenue service with black doors.
None of the painting diagrams I've seen for PM boxcars specify black paint for the roof or the ends, but those diagrams really can only be considered applicable to cars repainted by the PM itself. In "Revenue Freight Cars of the Pere Marquette", Art Million positively identified at least one series of cars (the 72000-series auto boxcars) as being delivered with black freight car cement on the ends. The texture in the photo bears this out.
One of the problems with determining the color of the ends is that color photos of PM freight cars in service are very scarce, and the lighting in a lot of old black and white photos wasn't good enough to distinguish a black end from an end that is in shadow.
Also, the way that freight cars weathered during the steam era can make it very hard to determine whether the car had a black roof and/or ends, or was just covered in cinder residue.
Two series of steel boxcars where the in-service photos I've seen occasionally show black ends clearly enough to make the case that some cars ran in revenue service with black ends are the 83500-83649 and 83800-83999 series.
When the PM repainted a car, it did it in the cheapest way possible- using a single body color. The roof and ends were then the same color. I'd bet that this is why I've seen later photos of cars from the 83500-83649 and 83800-83999 series which appear to have ends the same colors as the sides.
One example of a PM freight car paint job that many have accepted as common, but only lasted long enough for builder's photos, was that of the whitewashed 40-foot double-door auto boxcar #93499. All of the builder's photos show it in white or light gray with black lettering, but it was only painted that way for builder's photos and never left Ralston Steel Car Co. before it was repainted into the PM's freight car red color. A large print of this car's builder's photo (in whitewash) hung on the wall at Meyer's Hobby in Grand Rapids, Michigan for a couple of decades.
So, no, there is no real rhyme or reason to the appearance of black freigth car cement on the roof and/or ends of various series of PM boxcars. One thing that Is pretty certain form the photos I've seen is that once the PM got around to repainting cars at Wyoming or Saginaw, they simply used the side color on the roof and ends.
-Fritz Milhaupt, Publications Editor, Pere Marquette Historical Society, Inc.http://www.pmhistsoc.org