I'm backing up to s3 every 4 hours, with an s3.keep value of 100. However, it looks like old backups aren't being deleted, and I can't find the .yml file mentioned in other tickets, that backup uses to keep track of the number of backups.
I was having this problem as well, but my backup config was in a non-standard directory. Passing the root path into the perform command sorted this problem out for me:
backup perform -t daily --root-path /path/to/backup/
Config details here: https://github.com/meskyanichi/backup/wiki/Performing-Backups#command-line-options