Hi,
This took me a while, but I found the issue. So apparently it has something to do with shortcodes and timing of the index, but I don’t exactly know what the underlying cause is.
Luckily the solution is super simple, I just turned off this option under the index table settings. It caused many issues before, I suspect that during the editor “opening” process something happens with a custom field, which the plugin picks up as an “update” then somehow the IDs get mixed up under the hood in the WP core, but it’s only a guess.
I think I will put a massive warning sign on that option in the next update, it solves some issues on some installations, but causes a lot of problems in regular cases.