I tried to open "John" the Ripper from "K" menu\Backtrack\Priviledge Escalation\PasswordAttacks\PasswordOfflineAttacks\ John, and for a split second the Shell Konsole box opens up but then it closes. When I try to do the commands from just a plain shell konsole it still doesn't work properly because it isn't the John the Ripper program. I have tried both the Backtrack 3 ISO image and the VMWare image and both of them do the same thing. I have tried it on my Backtrack 2 VMWare image and it works like it is suppose to and gives me the passwords, so it must be a bug within Bactrack 3.
Like theprez says, which command are you running? If you ar trying to run start-john.sh either from the menu, or the command line, then you are correct. It's doesn't appear to be on the system. But, you should be able to cd /usr/local/john (or /usr/local/john-1.7.2) and run "john" there. You could even create your own "start-john.sh" with these commands.
I ran into the same problem, and here is how I got mine working. If you go into the KDE menu editor (right-click the kde 'start' button), and navigate to where John is (Backtrack>Privilege Escalation>) you have to change the command to:
and the workpath should be like:
make sure you check 'Enable launch feedback' and 'Run in terminal'
Then save and try it out. That should get it working from the KDE menu.