Are you really sure that you get root access and not that you see the content of the jail which looks like root as it contains folders with the same name then the web root? You can easily test that, login with ftp and create a file in the /root/ folder. Then login as root user with ssh and do a:
ls -la /root/
Do you get the file listed that you created with ftp? If not then you see the jail in ftp and not the root directory.