I figured out the missing door, an will post it in case any other newbies like me are lurking. Turns out, you can have a door in a wall on the second floor, but the door element is anchored to the first floor. It still looks normal in plan, but will not be visible in interior elevations. I found it when I was browsing in a 3D window and had my slab (floor) elements turned off.; that makes the problem really obvious. Fixing it was a simple matter of changing the story level of the door (and then I also had to change the base elevation to 0', as changing the story left the door in the same place, and changed its base elevation to -10'.