Look in your /etc/passwd file and find out what shell the web user is loading - somewhere near the end, it should say something along the lines of:
The key part there is the last bit /usr/sbin/jk_chrootsh which dictates what shell the user is presented with when they login. If it's not setup correctly, it will probably say /bin/bash or similar which basically means it's loading the normal unrestricted shell.
Regarding the "Jailkit Chroot Home" folder, I think that is the home folder INSIDE the chroot jail that the shell user will be taken to when they first login.
Also, turn on debugging then delete and recreate the client, the website, and the shell user. Then look in the logs and see if there are any errors when creating the jail.