Please check that you did not mix up customers and users. A customer can login to ISPConfig and manage his sites (and create system users on the tab "User & Email") but he cannot login to the system (e.g. by using FTP, email) because he is not a system user. A customer is an object that exists only in ISPConfig, but not on the system.
A system user cannot login to ISPConfig, but he can use services such as email, ftp, etc.