It took a while and it was starting at me in the face but I did figure it out. The script that starts the container would make changes to some php-fpm7 (fastcgi process manager) after it got started. Obviously, this did not take effect until the restart of the container. This explains the difference in behaviour. Thanks Francis Daly for all your insightful comments. Not being familiar with nginx I would have never figured it out without your input.