Hi,
If the "Force canonical URLs on listings" setting is not set to generate the URLs and save them, then it won't auto fill the canonical URLs.
The only things left I can think about area:
- a third party plugin/extension filling the canonical URLs automatically for some reason
- a mass action configured to fill the canonical URL automatically. Try to disable them.
I've tried to reproduce the problem on our end but I don't have it. If the option is turned off, I'm not able to have the "canonical URL" filled automatically.