Again, before I type my remarks, I appreciate your effort to get to a working system, I'm NOT a linux guru, I just google and ask questions to whoever I can...
I posted your configuration as a comment / question to the developer here, with some questions, regarding it. I like multiple answers (preferably the same) to solve a problem, as it is more reassuring.
- The time issue, I use NTP, configured as explained here, section 4.12. As I explained here, it takes my pi 15 minutes to synchronize time after a reboot, the solution (ntpcheck.sh, combined with the cron job and the dnsmasq option dnssec-no-timecheck) is the only thing that is reliable so far.
- If I understand you right, you are currently running one proxy (dnscrypt.eu-nl). I'm asking this, as it looks to me you would run into a possible problem when simply duplicating your configuration for the backup resolver.
First of all, according to this, there is NO SUCH THING as a backup resolver. The main page of pihole (graph forward destinations) proves them right.
Secondly, duplicating the configuration would overwrite (due to the setting -p /var/run/dnscrypt-proxy.pid) the pid file. Since I don't have this file, I cannot verify it, maybe I simply don't understand how this works. - In this topic (github), first entry, I list the output of the command sudo systemctl status -l dnscrypt-proxy@* (works for my configuration, using a service file and four socket files) In that listing, there is only one (of four) proxies that reports to be DNSSEC enabled (I've highlighted that line). I cannot even replicate this, running the command shows none of the proxies provide this message (doesn't mean they aren't DNSSEC enabled, dnscrypt-resolvers.csv says they are - this is one of the questions I asked the dnscrypt developer).
- Are you not using DNSSEC or simply not using the settings page of pihole (I never do).
If your NOT using DNSSEC, you can't help me, this is the core of my inquiries . If you do use DNSSEC, please count the number of SECURE, INSECURE, ABANDONED and BOGUS entries (notepad++ can help you here, it has a count button on the search dialog). Please count the entries of the previous day (pihole.log.1)
You haven't explained what all the settings in your configuration are doing and what you try to achieve with them.
Does your configuration allows for more then 2 proxies?