Ok, so more strange stuff.
If I add the command to the dnsmasq-4.conf file, and run the grep command, I get:
/etc/dnsmasq-4.conf:enable-ra
/etc/dnsmasq-4.conf:quiet-ra
/etc/dnsmasq.conf:enable-ra
/etc/dnsmasq.conf:quiet-ra
When I restart the service, the quiet-ra gets removed from the config file.