Changes to my Includes/Header.ss weren't working and doing the above still didn't clear the cache. This worked:
1 - copying to my desktop then removing the entire Includes folder from the server
2 - running /dev/build?flush=all
3 - manually removing all the files in the silverstripe-cache folder
4 - visiting the home page of the site with ?flush=1
5 - copying from the desktop to the server the entire Includes folder
6 - running /dev/build?flush=all
7 - manually removing all the files in the silverstripe-cache folder
8 - visiting the home page of the site with ?flush=1
I hadn't made changes to the SS files for several months, and it was a surprise to run into this issue where my simple change didn't get picked up. However, before I made my change to the Header.ss, I did a "duplicate" of the templates folder with my ftp client. Right after doing that my ftp client could not do a chmod to the templates folder, displaying an infrequent error the folder could not be found. Perhaps my ftp client changed a permission or something like that to mess things up.
SS is great. After hundreds of hours with Drupal and Joomla, SS is sane and has a great community. Thank you.