Cache issue with v4.1.2?

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Do you see anything in the following output?

Dec 28 12:36:30 dnsmasq[657]: query[A] dnscrypt.me from 192.168.5.147
Dec 28 12:36:30 dnsmasq[657]: forwarded dnscrypt.me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[657]: dnssec-query[DS] me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[657]: dnssec-query[DNSKEY] . to 127.0.0.1
Dec 28 12:36:30 dnsmasq[657]: reply dnscrypt.me is 104.31.74.114
Dec 28 12:36:30 dnsmasq[657]: reply dnscrypt.me is 104.31.75.114
Dec 28 12:36:30 dnsmasq[1351]: query[A] dnscrypt.me from 192.168.5.147
Dec 28 12:36:30 dnsmasq[1351]: forwarded dnscrypt.me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[1351]: dnssec-query[DS] me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[1351]: dnssec-query[DNSKEY] . to 127.0.0.1
Dec 28 12:36:30 dnsmasq[1351]: reply . is DNSKEY keytag 19036, algo 8
Dec 28 12:36:30 dnsmasq[1351]: reply . is DNSKEY keytag 20326, algo 8
Dec 28 12:36:30 dnsmasq[1351]: reply . is DNSKEY keytag 16749, algo 8
Dec 28 12:36:30 dnsmasq[1351]: reply . is DNSKEY keytag 2134, algo 8
Dec 28 12:36:30 dnsmasq[1351]: reply me is DS keytag 2569, algo 7, digest 1
Dec 28 12:36:30 dnsmasq[1351]: reply me is DS keytag 2569, algo 7, digest 2
Dec 28 12:36:30 dnsmasq[1351]: dnssec-query[DS] dnscrypt.me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[1351]: dnssec-query[DNSKEY] me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[1351]: reply me is DNSKEY keytag 59048, algo 7
Dec 28 12:36:30 dnsmasq[1351]: reply me is DNSKEY keytag 2569, algo 7
Dec 28 12:36:30 dnsmasq[1351]: reply me is DNSKEY keytag 53233, algo 7
Dec 28 12:36:30 dnsmasq[1351]: reply me is DNSKEY keytag 2735, algo 7
Dec 28 12:36:30 dnsmasq[1351]: reply dnscrypt.me is DS keytag 2371, algo 13, digest 2
Dec 28 12:36:30 dnsmasq[1351]: dnssec-query[DNSKEY] dnscrypt.me to 127.0.0.1
Dec 28 12:36:30 dnsmasq[1351]: reply dnscrypt.me is DNSKEY keytag 2371, algo 13
Dec 28 12:36:30 dnsmasq[1351]: reply dnscrypt.me is DNSKEY keytag 34505, algo 13
Dec 28 12:36:30 dnsmasq[1351]: validation result is SECURE
Dec 28 12:36:30 dnsmasq[1351]: reply dnscrypt.me is 104.31.75.114
Dec 28 12:36:30 dnsmasq[1351]: reply dnscrypt.me is 104.31.74.114

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With DNSSEC enabled, same issue (no caching) with Quad9 (filtered, DNSSEC) 9.9.9.9 and 149.112.112.112.
But ... Quad9 (filtered, DNSSEC) 2620:fe::fe is ok, Pi-hole cache is working.

Above tested with FTL v4.1.1

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There should be a large block of output that details the cache.

Dec 28 16:42:02 dnsmasq[15343]: time 1546015322
Dec 28 16:42:02 dnsmasq[15343]: cache size 10000, 0/230972 cache insertions re-used unexpired cache entries.
Dec 28 16:42:02 dnsmasq[15343]: queries forwarded 67794, queries answered locally 57024
Dec 28 16:42:02 dnsmasq[15343]: queries for authoritative zones 0
Dec 28 16:42:02 dnsmasq[15343]: DNSSEC memory in use 16192, max 23980, allocated 440000
Dec 28 16:42:02 dnsmasq[15343]: server 149.112.112.112#53: queries sent 44183, retried or failed 1033
Dec 28 16:42:02 dnsmasq[15343]: server 9.9.9.9#53: queries sent 31377, retried or failed 960
Dec 28 16:42:02 dnsmasq[15343]: Host                                     Address                        Flags      Expires
Dec 28 16:42:02 dnsmasq[15343]: smarthomeshopper.com           ::                                       6F I   H
<snip extensive list of domains in cache>
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