Jobs in /etc/cron.daily are running fine, however they don't show up in Webmin's cron section. I'm guessing Webmin just isn't scanning the cron.daily directory and therefore isn't showing jobs in there? Looks like this issue has been around for a while: https://virtualmin.com/node/21957 . Would be great to get this fixed so all current cron jobs are visible in Webmin.
Some other folders that should be included too (in case they already aren't):
cron.hourly cron.monthly cron.weekly