I discovered that their shell was set to /bin/false.
So I changed it manually:
usermod -s /usr/sbin/jk_chrootsh site1
Do not modify an ispconfig user manually. The only thing that you can achieve with that is to break your setup. Please delete the users and sites that you modified manually in ispconfig and recreate them afterwards in ispconfig.
Jailkit is working fine in ispconfig 3.0.2, so we have to find out whats wrong with your installation. Have you installed jailkit before you installed ispconfig or after you installed ispconfig.