Hi,
i had the same problem here
as posted in my last comment.
Try out
in /etc/pihole/setupVars.conf
PIHOLE_INTERFACE=eth0
PIHOLE_INTERFACE=tun0
make a new file in /etc/dnsmasq.d and call it 02-pihole-own.conf
Write in this file just 3 lines
interface=eth0
interface=tun0
interface=lo
check /etc/dnsmasq.conf and /etc/dnsmasq.d/* for a file with
except-interface=nonexisting
if this is in a file, delete it.
After that reboot the container, pihole restartdns is not enough here.
I'm not sure why this changes is needed now, on my old jessie containers it worked a long time but on stretch it works at this way only