When I enable the option to "Fill burner structures" it works until something triggers a "Recheck all entities" which then breaks the filling of burner structures, but turrets and so on seem to work fine still. This is on a modded bobs/angels game but still happens if I disable all mods.

You can easily replicate it by pressing ctrl+shift+alt+backspace ingame and it will break for burners. The only way I found to get it working again is to replace all burner structures, which only lasts until the entities get checked again. Regardless to say this becomes very annoying as it seems when I change mod settings and so on it triggers this.

Here is screenshots of the issue:
https://imgur.com/a/Esk9glk

Save file:
https://drive.google.com/open?id=1y3wk9boc5DglouPUrYejKT5FP9W3qnYO

I am having the same issue, also no mods installed except Ammo Loader+ on a new game.
Factorio 0.17.66 - Steam

Hi, thanks for taking the time to report this issue!

This looks like it is due to an amateur oversight in the code on my part. I'm currently working on an update, and I'll include a fix for this along with the other bugfixes I'm working on. Sorry for the inconvenience, it really is something I should have caught before now.

The update should be out tonight or tomorrow morning.

I just uploaded the new version. Sorry it took so long, I had some other features I've been trying to roll out for a while that took longer than expected. Let me know if you still have trouble after updating.