I made some more tests and found the following. Looking to the script /usr/local/ispconfig/server/scripts/create_jailkit_user.sh I made the commands listet there directly from the shell, so I did:
useradd -g 5006 -u 5005 -o shtest
jk_jailuser -n -s /bin/bash -j /var/www/clients/client5/web5/ shtest
After these two lines everything is written correctly. Seems that some other commands make the entries in the passwd file wrong afterwards.