[Dovecot] Courier to dovecot migration issue

Hello, I am trying to migrate users form courier to dovecot 1.2.6. The main configuration parameters are as follows :

# 1.2.6: /usr/local/etc/dovecot.conf Warning: fd limit 1024 is lower than what Dovecot can use under full load (more than 2304). Either grow the limit or change login_max_processes_count and max_mail_processes settings # OS: Linux 2.6.16-1.2133_FC5 i686 Fedora Core release 5 (Bordeaux) base_dir: /usr/local/var/run/ log_path: /var/log/dovecot.log info_log_path: /var/log/maillog protocols: imap imaps pop3 pop3s ssl: no disable_plaintext_auth: no login_dir: /usr/local/var/run//login login_executable(default): /usr/local/libexec/dovecot/imap-login login_executable(imap): /usr/local/libexec/dovecot/imap-login login_executable(pop3): /usr/local/libexec/dovecot/pop3-login max_mail_processes: 2048 verbose_proctitle: yes first_valid_uid: 100 last_valid_uid: 1000000 mail_location: maildir:~/Maildir:INDEX=/tmp/QUOTA/index/%u:CONTROL=/tmp/QUOTA/control/%u mail_debug: yes mail_executable(default): /usr/local/libexec/dovecot/imap mail_executable(imap): /usr/local/libexec/dovecot/imap mail_executable(pop3): /usr/local/libexec/dovecot/pop3 mail_plugins(default): quota imap_quota mail_plugins(imap): quota imap_quota mail_plugins(pop3): mail_plugin_dir(default): /usr/local/lib/dovecot/imap mail_plugin_dir(imap): /usr/local/lib/dovecot/imap mail_plugin_dir(pop3): /usr/local/lib/dovecot/pop3 namespace: type: private prefix: INBOX. inbox: yes list: yes subscriptions: yes auth default: passdb: driver: pam args: * userdb: driver: passwd plugin: quota: fs:acad_proto

After using the "courier-dovecot-migrate.pl" script users using pop3 are re-downloading their old emails as duplicates. This issue is resolved by replacing : maildir:~/Maildir:INDEX=/tmp/QUOTA/index/%u:CONTROL=/tmp/QUOTA/control/%u

with

maildir:~/Maildir

any idea on the reason of these duplicates or workarounds to prevent them while keeping indexes in /tmp.

Thank you.