Thanks for showing me where the issue is!
For some reason, even though /etc/init.d/mydns start/restart/stop appears to work, when I check my active processes, I don't see myDNS anywhere. I reconfigured with the newest version, and although myDNS will say it's starting, it doesn't, so I'm attempting to work that out. At least I don't have to focus on dnsmasq or the way I've set my configurations, now that I know the problem lies with myDNS. Any additional suggestions would also be appreciated, though I'm currently researching what may cause this behavior now.