I saved the output of some commands with non-working 5.9 and reinstalled with 5.8 and did the same again.
Below are the diffs, the config I used is the same but something certainly changed between 5.8 and 5.9. # diff of "route -n get -inet6 fe80::a00:27ff:fe33:981e%gre0" --- route_gre.58 Wed Jun 22 08:45:26 2016 +++ route_gre.59 Wed Jun 22 10:33:51 2016 @@ -1,9 +1,10 @@ route to: fe80::a00:27ff:fe33:981e%gre0 -destination: fe80::%gre0 - mask: ffff:ffff:ffff:ffff:: - interface: gre0 - if address: fe80::a00:27ff:fe2f:9737%gre0 - priority: 4 (connected) - flags: <UP,DONE> +destination: fe80:: + mask: ffc0:: + gateway: ::1 + interface: lo0 + if address: ::1 + priority: 8 (static) + flags: <UP,GATEWAY,REJECT,DONE,STATIC> use mtu expire - 0 0 0 + 2 32768 0 # diff of simple “ifconfig" --- ifconfig.58 Wed Jun 22 08:44:09 2016 +++ ifconfig.59 Wed Jun 22 10:31:40 2016 @@ -1,33 +1,33 @@ lo0: flags=8049<UP,LOOPBACK,RUNNING,MULTICAST> mtu 32768 - priority: 0 + index 4 priority 0 llprio 3 groups: lo - inet6 fe80::1%lo0 prefixlen 64 scopeid 0x4 inet6 ::1 prefixlen 128 + inet6 fe80::1%lo0 prefixlen 64 scopeid 0x4 inet 127.0.0.1 netmask 0xff000000 em0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> mtu 1500 lladdr 08:00:27:2f:97:37 - priority: 0 + index 1 priority 0 llprio 3 groups: egress media: Ethernet autoselect (1000baseT full-duplex) status: active inet 10.0.2.15 netmask 0xffffff00 broadcast 10.0.2.255 em1: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> mtu 1500 lladdr 08:00:27:2c:f6:cf - priority: 0 + index 2 priority 0 llprio 3 media: Ethernet autoselect (1000baseT full-duplex) status: active inet 10.0.0.1 netmask 0xfffffffc broadcast 10.0.0.3 inet6 fe80::a00:27ff:fe2c:f6cf%em1 prefixlen 64 scopeid 0x2 enc0: flags=0<> - priority: 0 + index 3 priority 0 llprio 3 groups: enc status: active -pflog0: flags=141<UP,RUNNING,PROMISC> mtu 33192 - priority: 0 - groups: pflog gre0: flags=9011<UP,POINTOPOINT,LINK0,MULTICAST> mtu 1476 - priority: 0 + index 5 priority 0 llprio 3 groups: gre tunnel: inet 10.0.0.1 -> 10.0.0.2 - inet6 fe80::a00:27ff:fe2f:9737%gre0 -> prefixlen 64 scopeid 0x6 + inet6 fe80::a00:27ff:fe2f:9737%gre0 -> prefixlen 64 scopeid 0x5 inet 10.10.0.1 --> 10.10.0.2 netmask 0xfffffffc +pflog0: flags=141<UP,RUNNING,PROMISC> mtu 33188 + index 6 priority 0 llprio 3 + groups: pflog # diff of "netstat -nrf inet6" --- netstat.58 Wed Jun 22 08:44:39 2016 +++ netstat.59 Wed Jun 22 10:32:48 2016 @@ -2,9 +2,9 @@ Internet6: Destination Gateway Flags Refs Use Mtu Prio Iface -::/104 ::1 UGRS 0 0 32768 8 lo0 ::/96 ::1 UGRS 0 0 32768 8 lo0 -::1 ::1 UHl 14 0 32768 1 lo0 +::/104 ::1 UGRS 0 0 32768 8 lo0 +::1 ::1 UHl 3 3 32768 1 lo0 ::127.0.0.0/104 ::1 UGRS 0 0 32768 8 lo0 ::224.0.0.0/100 ::1 UGRS 0 0 32768 8 lo0 ::255.0.0.0/104 ::1 UGRS 0 0 32768 8 lo0 @@ -13,19 +13,17 @@ 2002:7f00::/24 ::1 UGRS 0 0 32768 8 lo0 2002:e000::/20 ::1 UGRS 0 0 32768 8 lo0 2002:ff00::/24 ::1 UGRS 0 0 32768 8 lo0 -fe80::/10 ::1 UGRS 0 0 32768 8 lo0 +fe80::/10 ::1 UGRS 0 2 32768 8 lo0 +fec0::/10 ::1 UGRS 0 0 32768 8 lo0 fe80::%em1/64 fe80::a00:27ff:fe2c:f6cf%em1 UC 0 0 - 4 em1 -fe80::a00:27ff:fe2c:f6cf%em1 08:00:27:2c:f6:cf UHLl 0 0 - 1 lo0 -fe80::%lo0/64 fe80::1%lo0 U 0 0 32768 4 lo0 +fe80::a00:27ff:fe2c:f6cf%em1 08:00:27:2c:f6:cf UHLl 0 0 - 1 em1 fe80::1%lo0 fe80::1%lo0 UHl 0 0 32768 1 lo0 -fe80::%gre0/64 fe80::a00:27ff:fe2f:9737%gre0 U 0 0 - 4 gre0 -fe80::a00:27ff:fe2f:9737%gre0 fe80::a00:27ff:fe2f:9737%gre0 UHl 0 0 - 1 lo0 -fec0::/10 ::1 UGRS 0 0 32768 8 lo0 -ff01::/16 ::1 UGRS 0 0 32768 8 lo0 +fe80::a00:27ff:fe2f:9737%gre0 fe80::a00:27ff:fe2f:9737%gre0 UHl 0 0 - 1 gre0 +ff01::/16 ::1 UGRS 0 2 32768 8 lo0 ff01::%em1/32 fe80::a00:27ff:fe2c:f6cf%em1 UC 0 0 - 4 em1 -ff01::%lo0/32 ::1 UC 0 0 32768 4 lo0 +ff01::%lo0/32 ::1 UC 0 1 32768 4 lo0 ff01::%gre0/32 fe80::a00:27ff:fe2f:9737%gre0 UC 0 0 - 4 gre0 -ff02::/16 ::1 UGRS 0 0 32768 8 lo0 +ff02::/16 ::1 UGRS 0 2 32768 8 lo0 ff02::%em1/32 fe80::a00:27ff:fe2c:f6cf%em1 UC 0 0 - 4 em1 -ff02::%lo0/32 ::1 UC 0 0 32768 4 lo0 +ff02::%lo0/32 ::1 UC 0 1 32768 4 lo0 ff02::%gre0/32 fe80::a00:27ff:fe2f:9737%gre0 UC 0 0 - 4 gre0