I tried to reproduce this locally but haven't been able to get the wrong/strange behavior.
Please add
DEBUG_QUERIES=true
DEBUG_FLAGS=true
to your /etc/pihole/pihole-FTL.conf
and run pihole restartdns
. This will put FTL into (very verbose!) debugging mode. Please provide snippets from the file /var/log/pihole-FTL.log
when it works and when it doesn't