I am giving up. I cannot fix this. I will do a new install and give Kloxo-MR another try. I really wish I stick with it because it's free. But I can't keep on messing with it. I have all my websites in one vps. If new install doesn't workout then it's time to go back to cPanel when I hate to pay for it. But it's stable.
By the way what is the best way to backup all clients/domains/reseller/accounts. Like backup even mails that are on the server. So once the new install is done I can restore them back with password and everything. Is possible? I know cPanel has that option.