chkrootkit was upgraded and along with the upgrade comes a change in the configuration file location. The old location was under /etc. The new location is under /etc/chkrootkit. After the upgrade, you'll end up with two configuration files. All you need to do is delete the file under /etc; e.g. /etc/chkrootkit.conf. Of course, you need to delete the file with sudo or su privileges.