Got it fixed! Thanks for the help!
The tip about the auto build wall was exactly right. If I looked at a doll house view of the 1st floor, that wall was two stories tall (after I built the roof, but not before). And the tip for looking in the attic (where I did not build walls so would never have guessed to look there!) let me find the problem - maybe. I still don't understand what happened exactly. I will explain just in case this will help someone else.
After I built the walls, I added breaks in them so that I could have a surface material on the edges and not all the way across. All seemed well until I built the roof as I originally explained. After the suggestion of looking in the attic, I zoomed way in and found that the wall lines were not exactly straight (see #1 in the picture). What I don't understand is that these not straight parts were in the middle of wall segment pieces (which I had not moved) and not where the walls had a break. As you can see in the picture, the lines are all but straight; it was such a small detail that could only be seen with extreme zooming. I deleted all three sections of the 2nd floor, and added a single wall back in. I added widows and wall breaks and then rebuilt the roof - just like I did the first time - but this time, no more windows filled with wall.
