I have encountered various problems with timeouts Courier Imapd that I never did with Dovecot, after upgrading to a newer version of ISPConfig 2. Of course there may be many reasons for this, but so far the results seem good, no sign of timeouts. I thought I should therefore post my procedure here in case it helps someone.
Remember this is JUST for removing Courier Imapd on Ubuntu 9.10 Karmic Koala and replacing it with Dovecot.
To perform this procedure, you must be logged on to the server in question as root
1. Remove Courier
(Y to accept proposed solution), Y again
2. Install Dovecot IMAP and POP3 servers
aptitude remove courier-base
3. Enable logon without TLS/SSL in Dovecot, by adding (or changing) this line to /etc/dovecot/dovecot.conf
aptitude install dovecot-imapd dovecot-pop3d
disable_plaintext_auth = no
then restart Dovecot to make the change live
service dovecot restart
That's it, you should now have a working POP3/IMAP server, but running on Dovecot instead of Courier. You may now also find that you can have IMAP folders on the same level as the Inbox without having to jump through hoops!
I hope this procedure helps someone.