Hi there and Hi Fludi!
Why "seems not to block"? Is it because there is no infomation in your "Dashboard" and "Query-Log" within webinterfae?
If so, I may have the exact same issue.
Came here by googleing for "FATAL: Trying to free NULL pointer in pihole_log_flushed()" and had similar entries in my debug output regarding "IPv6 not matching the IP from /etc/pihole/setupVars.conf".
Both are also present in Fludi's debug.
Sorry for hijacking this! But I would be pleased to help and get helped in one place. 
My PiHole seems to block domains as expected but doesn't hold a persistant log anymore or at least not in a way that it is available within the webinterface. "Dashboard" and "Query Log" don't show any entries.
No idea since when exactly this is the case (because it seems to still block). Might be after updating to current master version a few weeks ago.
pihole -v
Pi-hole version is v3.3 (Latest: v3.3)
AdminLTE version is v3.3 (Latest: v3.3)
FTL version is v3.0 (Latest: v3.0)
I managed to solve the "IPv6 not matching" issue by editing "/etc/pihole/setupVars.conf" and correcting PiHole's IPv6 to a value my router (Fritz Box 7490 whith activated DHCP) assigns to my PiHole.
I've ensured that ULA is activated on my router andI tried several "repairs" and reboots, but still no query-logging in webinterface, although "pihole tail" works properly.
And there is always the follwing entry in my debug:
FATAL: Trying to free NULL pointer in pihole_log_flushed() (flush.c:61)
as well as
[2018-03-14 19:42:23.578] Reading from /var/log/pihole.log (rw-r--r--)
[2018-03-14 19:42:50.015] FATAL: FTL received SIGTERM from PID/UID 7392/0, exiting gracefully
[2018-03-14 19:42:50.015] Shutting down...
So... Is this similiar to Fludi's issues? Could it be that FTL and logging are resonable causes?
My current debug token is: ngqopsxrt6