Sounds a bit like the interface is reported a bit late.
Check dmesg.
Could be driver issue.
Not sure if works but for diagnosing, you could try delay pihole-FTL a bit by editing below file:
sudo nano /etc/init.d/pihole-FTL
And squeeze in a sleep command (30 seconds just to be sure 
) somewhere here:
#!/bin/bash
### BEGIN INIT INFO
# Provides: pihole-FTL
# Required-Start: $remote_fs $syslog
# Required-Stop: $remote_fs $syslog
# Default-Start: 2 3 4 5
# Default-Stop: 0 1 6
# Short-Description: pihole-FTL daemon
# Description: Enable service provided by pihole-FTL daemon
### END INIT INFO
sleep 30
FTLUSER=pihole
PIDFILE=/var/run/pihole-FTL.pid
[..]