For me, the culprit is the collapsible comments mod (or the standalone script if you're using that one).
edit: The root cause seems to be lines 182 to 190. But the actual troublemaker appears to be on kbin's side, not KES. When the mod's main function finishes, the comment still only has only one .more element like when it began.
I've disabled all other mods and userscripts, so it's not one of those. Also just tried to disable KES (and even the monkey) entirely, running the script from the console instead. No change either, it's still happening.
The code fragment in question copies the comment into a new children container. I'm thinking this probably makes some part of kbin confused, leading to the issues we're seeing.
It might be best to just include the userstyle I'm using in the CSS added by the mod.
This is the code between lines 182 and 190, removing which prevents the issue:
let children = previousComment.querySelector('.children');
if (!children) {
// If not, create one
children = document.createElement('div');
children.className = 'children';
previousComment.appendChild(children);
}
// Insert comment into children container
children.prepend(comment);