When running rebuildrecentchanges.php, it cuts all revisions off of the recent changes list. It does this because it thinks that all revisions are bot edits, even if they are not, and if the users are not. Removing this stage manually from rebuildrecentchanges.php eliminates the problem.
Additionally, the script also removes tags from recent changes, such as the VisualEditor tag. I am not sure how to change the script to get this working; it seems more difficult than the bot issue nnabove.
This is on MediaWiki 1.31, built using the official MediaWiki container on CoreOS.