Did you install the complete setup incl ISPConfig?
Then there are 2 solutions.
1) Use mailbox instead of maildir as the howto installs a pop3 daemon that is only capable of managing mails in mbox format. You will have to disable the maildir checkbox in ISPConfig under management > server > settings on the mail tab.
2) If you want to use maildir, which is faster then mbox and more stable then mbox, you will have to enable the maildir checkbox in ISPConfig under management > server > settings on the mail tab and install the dovecot pop3 and imap package instead of the pop3 daemon used in the howto.
apt-get install dovecot