Recently, we saw a number of issues regarding a failed cPanel upgrade that involved the Mail and FTP server. It looks like an incorrect value was updated in the cpanel.config file for the mail server and FTP server. In order to correct this:
1) Login to WHM
2) Change mail server to something other than what it is currently and then save
3) Change it back to the original mail server setting and save
4) Change FTP server to something other than what it is on and save
5) Change it back to original ftp server setting and save
6) Kick off /scripts/upcp in a screen on the server
Alternatively for you command line lovers you can use the following scripts from the /scripts directory.
For instance if you wanted to fix the mail server to force a reinstall of courier you would use
/scripts/setupmailserver courier --force
that would force a reinstall of the courier subsystem and enable/start it.
Also, you can add these two lines to the bottom of /var/cpanel/cpanel.config:
replacing each $SERVER variable with the server in use.