Thank IgorG,
I ended up resetting the server to default and bringing everything back. Works great now.
For anyone with similar problem on a newly configured server I brought back the massages from each user's /old//var/qmail/mailnames/<domain_name>/<mail>/Maildir/cur/ directory, reset...
I recently had to reset my server to its default LAMP and in the process of migrating everything back I used rsnyc to move /old/qmail to /var/. This was done after email accounts were set in plesk. The good new was that all emails and folders migrated successfully however now email clients can...