you made one mistake, in the installation manual http://www.ispconfig.com/manual_installation.htm
you missed step 7 which I quote here:
In step 7 ("Encrypting RSA private key of CA with a pass phrase for security [ca.key]")and step 8 ("Encrypting RSA private key of SERVER with a pass phrase for security [server.key]") of the certificate creation process you are asked if you want to encrypt the respective key now. Choose n there because otherwise you will always be asked for a password whenever you want to restart the ISPConfig system which means it cannot be restarted without human interaction!
I guess there is a way to recreate your sssl certificates, do a search on the forum and find a post like this with exactly the same problem: