Hi, I think I have a similar problem.
I created a client, then a website and at least, at shell account with a Jailkit chroot.
Its dir is `/var/www/clients/client1/web1`. When I login, I'm located in `/var/www/clients/client1/web1/home/[clientname]`. I can browse the whole filesystem (according to the user permissions at least).
A last thing, I let the username empty because a shell login with [clientname] was fine. Could it be related? No chroot created because of no username given?
PS: I've installed Jailkit before ISPConfig ;-)