[Dovecot] Courier to dovecot migration issue

[Rami Rami]

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.