I'm uhh.. definitely a "coder". Extensive development history. I'm okay with taking on the task here, I'll keep digging. I have one month. I have to have a cure before next term. We create those courses (with my software of course) by backing up original templated course, then restore into the new term courses, one for every time slot we teach that course in. That mechanism is the only way we can make this school run efficiently. It would be a zoo gone wild, without it. It's a CLI script. So I'm going to write a companion script to test backup that way. Perhaps there will be a different behavior than interactively.
Lucky for me, with PHP you can output anywhere in the code using echo command. I find this is a huge huge tool for solving problems. echo "hello world"; or, better yet echo "<h1>hello world</h1><br />"; if you really want to see it. Anyway, back to the problem at hand.
So I looked in the temp folder and found one of those logs that had text in it. The rest didn't. Perhaps this is a clue. I've included that log in this reply.