When upgrading your installation, it might happen that DokuWiki continues to show the update message, even though the number in conf/msg was increased by the upgrade. This is because DokuWiki caches already fetched messages for a day and will only refetch if the last modified timestamp of conf/msg is higher than the one of the cache file. To stop the outdated update message from showing you can simply wait a day, touch1) the conf/msg or delete the data/cache/messages.txt cache file.
The cache directory was emptied.
It's been days.