Q: Does ISPC run it's own scan and update for rkhunter or are these run by cron.daily and cron.weekly. also I want to disable rkhunter from sending emails, but I can't seem to get it right.
Ispconfig runs its own nightly scan. But this scan gets stored in the databse only an ddoes nots end any emails, except you reconfiguerd rkhunter manually to send emails.
rkhunter will send email by default if it senses an error. Usually the error message doesn't say much. The best way to get it to stop sending the email is to fix the error. If you update any of the files it checks you need to run rkhunter --propupd or it will sense the changes as errors. Another error it detects often is when it can't reach the server to update itself. I did some hacking so it only updates once a week rather than nightly.
