Are you using 0.5.1? I just recently updated my server from 0.5 to 0.5.1, and we're having the same problem. Despite the fact that my configuration has the following settings, they are no longer taking effect since the update. Each user has to individually set these configuration options through the interface. It's making me a very unpopular person at the office. Not to mention wasting a lot of my time holding everyone's hand while they change their settings. :-(
// store draft message is this mailbox
// leave blank if draft messages should not be stored
$rcmail_config['drafts_mbox'] = 'Drafts';
// store spam messages in this mailbox
$rcmail_config['junk_mbox'] = 'Junk';
// store sent message is this mailbox
// leave blank if sent messages should not be stored
$rcmail_config['sent_mbox'] = 'Sent';
// move messages to this folder when deleting them
// leave blank if they should be deleted directly
$rcmail_config['trash_mbox'] = 'Trash';
// display these folders separately in the mailbox list.
// these folders will also be displayed with localized names
$rcmail_config['default_imap_folders'] = array('INBOX', 'Drafts', 'Sent', 'Junk', 'Trash');
// automatically create the above listed default folders on login
$rcmail_config['create_default_folders'] = true;
// protect the default folders from renames, deletes, and subscription changes
$rcmail_config['protect_default_folders'] = true;