10. Reconfigure Network Manager to use DNSCrypt
Open Network Connections from the menu. On the Wired or Wireless tab highlight your active Internet connection. Click "Edit". On the IPv4 Settings tab, set Method to "Automatic (DHCP) addresses only" and set DNS servers to "127.0.0.1". Click "Save". Click "Close".
This is not how the "DNS servers" field is supposed to be used. The DNS server addresses listed in that field are supposed to be the addresses of servers accessible over that connection
What you really want to do is to reconfigure the resolver so that it only uses dnscrypt-proxy and not any other nameservers known to the system, including nameservers known to NetworkManager.
Sooner or later dnscrypt-proxy will be packaged for Debian (http://bugs.debian.org/692320
) and shortly there will be support for dnscrypt-proxy in dnsmasq (ugs.debian.org/709179).
Until that work is done, on a system with resolvconf, the best thing to do is to put
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nameserver 127.0.0.2 # dnscrypt-proxy's listen address