when I go to my User mail in webmin and send an email to myself it does not appear there. It does appear though under my username in /var/mail, although I have configured dovecot to use ~/Maildir.
What am I doing wrong? – Any help is much appreciated.
You haven’t told us your MTA, so I’ll guess Postfix. What’s the mailbox_command in /etc/postfix/main.cf? If nothing or anything other than dovecot-lda, Dovecot has nothing to do with where mail is delivered.
Are you using Virtualmin? If so, you’ve got a messed up Postfix configuration. It should be using procmail to deliver mail, if you want any of the Virtualmin forward/autoresponder/spam/AV features.