While it's good in a way to hear that the bug has gone away, it's still a bit worrying that you experienced it in the first place.
It's not something I've ever seen before and we do a lot of prototype editing here. And with several thousand sites running CodeRunner and no-one having reported a problem like this before, I think it has to be a very rare problem. It's rarity suggests some sort of race problem but then on the other hand it was very consistent for you over a period of time, which isn't normal for race problems.
I've pored over the source code and the only potential trouble spot I can see is in the author form's use of jQuery, which is now deprecated in Moodle. But jQuery must have been working for you to be able to customise the form. So ... I'm still baffled.
To eliminate at least that one potential cause if the problem ever recurs, I've changed authorform.js to remove all use of jQuery. I'll push the change to the development branch on github but it will likely be some time before it appears in the master branch.
Please report back if the bug reappears.