Before we can find a solution we will have to find out what happened as neither the ispconfig nor jailkit developers had been able able to reproduce this until now.
1) What exactly did you do on the server before this happened?
Please boot the system from a rescue CD, then mount the harddisk and send me a copy of /etc/passwd and /etc/group by email to dev [at] ispconfig [dot] org
Then chroot to the system and execute the command:
and send me the output.