I'm running 16.6 P004 and have exactly the same problem.
One design will work and another won't. Can't see a common factor that might be the problem.
When it doesn't work, the display order does not follow the preferences set up in "layer-priority" when printing. I've disabled custom colrs in the color dialog (I have color overrides on some nets) and I've set the active subclass to one that is not displayed (following clues in the help file).
Anyone care to step up to the plate on this one?