I am making changes to php files and they are not showing -- sometimes. Sometimes they will show immediately. Sometimes I have to wait a few minutes. I've gone through and turned off all the cache that I could think to turn off. The problem is inconsistent and tough to duplicate consistently.
Answering my own question...
I spent quite awhile doing trials to consistently reproduce the behavior. I had to let the server sit without refresh any page for a few minutes. Then if I change the file before I refresh the page, the change show immediately and all subsequent changes show immediately. If I refresh the page first, then make a change to the file, then no subsequent changes show until I refresh 10-20 times, or so.
BTW, html files show all updates regardless, so it was a php issue.
Before finding the answer, I tried...
sendfile off;expires off;... none of these work. I then found that it was in fact OPcache. I fixed the issue by changing the php.ini file to this (and restarting all services)
opcache.enable=0