I installed the current version chrony:amd64/jessie 1.30-2 uptodate in a virtual machine and was not able to fault it's start up.
The script in /etc/init.d/chrony appears to be working fine. I am using systemd and I am not even sure the script /etc/init.d/chrony is even used now? I suggest that no update has happened on this for several years and there is no sign of the bug in the current release it be closed. Otherwise please submit some details . e.g. /etc/chrony/chrony.conf plus network set up. Andrew