Just discovered something.  I may have been too POed to notice the obvious.  I had been hoping that it was something like this. 
When you click on a folder with a ? on it there's a button that appears at the end of the folder name.  That button is a refresh button that forces a scan of the folder.  The button is a long ways from being obvious.  It has a small circular arrow which I had assumed was telling me that it was working on scanning the folder.
Still not sure why they don't have it automatically scan the folder when there's a request to open it but I'll settle for usability even if it is more than a bit clunky.