KellyCC

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.  

I have two stories.  In one wall there are windows upstairs and matching windows downstairs.  Everything looks perfect till I build the roof.  Then the upstairs windows fill with wall.  The windows are still there but instead of see through glass, there is exterior wall. 

I checked that the upstairs wall is aligned with the downstairs wall.

If I delete the roof I can see through the windows again. 

Or if I rebuild the roof which refills the windows, I can delete the downstairs wall and the upstairs windows return to see through/normal.  I rebuild the wall and the problem returns.

This is the only place in the house where this is happening.  I have compared the upstairs and downstairs settings on the Room Specification Dialog >Structure to other rooms in the house and they are identical.

Any suggestions?