Verify config files: If you also installed DNScrypt, as explained in this topic (the instructions are a little outdated, I used version 1.8.1, not version 1.7.0 as mentioned in the instructions), you will NOT have server settings in /etc/dnsmasq.d/01-pihole.conf and /etc/pihole/setupVars.conf. The instructions to install DNScrypt require you to comment out these settings. The comment lines ('#server=' and '#piholeDNS=') are removed, as you upgrade pi-hole.