Finally this was a server misconfiguration. I put the solution here for everyone who read this post:
I run apache on a mac web server. It's typical apache, and I administer it via CLI, just like a normal web server, however every once in a while, Apple does something different. When you said that I should look at the "default ssl" file, I looked but could not find it. So I went to the GUI, to see if there was some sort of indication there. I looked up the config for the site that was working, and found that there are checkboxes for the site, as follows.
Those were checked on the functioning site, but not on the others. Once I enabled those boxes, they began to work!