I was having the same difficulty. Thanks!
I wonder if we could request a feature for the admin control panel to call jk_update so once I've fixed the jk_init.ini file I can tell the control panel to fix either all or just individual jails.
For now, after fixing jk_init.ini, I just use:
jk_update -j /var/www/clients/clientx/webx
and the problems I've been having go away.
Luckily I only have a couple of jails, but I'd imagine it would be tedious if there were more. By the way, if you are using a 32-bit version of Ubuntu the directory starts with i386 not x64.
Thanks for the help!