You may want to add:
proxy-dnssec
to the dnsmasq.conf.add file if you plan to use dnssec.
Edit: I decided to add to this post instead of creating another...
Several folks have had the same "issue" with Stubby install recently. Everything one needs is in the Github post
Code:
https://github.com/Xentrk/Stubby-Installer-Asuswrt-Merlin
One should not attempt to install Stubby without reading the instructions first.
If you do not understand a procedure, ask first.
For Windows users I recommend you get and install on your PC WinSCP and Putty. WInSCP is a great tool for browsing and editing files on a remote device such as an Asus router. Putty is needed to issue commands and check if processes work.
Some other things you need to know:
The Stubby Installer disables DNSSEC in Merlin. There is some debate if you really need DNSSEC if you have encrypted DNS provided by Stubby. So, it is you choice to turn DNSSEC back on or not.
Enabling DNSSEC will break the Cloudflare help test.
Most DNSSEC tests on the web only check if the remote resolver is capable of DNSSEC not that your DNSSEC is working. Using Dig is about the only way to test your connection. Yes, there are iOS and Android apps for this.
DNSSEC can be enabled in Stubby or Merlin (dnsmasq). Either work and neither is preferred. At this time I'm using Clean Browsing Security DNS with DNSSEC enabled in Merlin.
As a temporary fix for the time server issue you can use an IP address of a time server in NTP Server setting. Although the fix to /jffs/configs/dnsmasq.conf.add is preferred.