Hi @tadej
Have you tried to reproduce the issue on one of the WordPress’ stock themes (like Twenty Sixteen) with only ACF activated? It’s possible that there’s a new code that modifies the repeater query, thus caused the update issue.
If the issue persists, could you please open a new ticket and provide temporary admin credentials to your site? You can open a new ticket here: https://support.advancedcustomfields.com/new-ticket. Also, please don’t forget to explain the issue again and provide the link to this thread.
Thanks 🙂