Federation fails when using a DNS server on a link-local IPv6 address

[matrixbot]

This issue has been migrated from #5846.

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Our Matrix instance nitro.chat has issues connecting to matrix.org rooms. In the logs we see these messages:

2019-08-12 16:51:28,877 - synapse.crypto.keyring - 652 - INFO - POST-104458- Requesting keys dict_items([('matrix.org', {'ed25519:auto':1565621488877})]) from notary server matrix.org
2019-08-12 16:51:28,879 - synapse.crypto.keyring - 604 - WARNING - POST-104458- Key lookup failed from 'matrix.org': Failed to connect to remote server
2019-08-12 16:51:28,880 - synapse.http.matrixfederationclient - 404 - INFO - POST-104458- {GET-O-3981} [matrix.org] Sending request: GET matrix://matrix.org/_matrix/key/v2/server/ed25519%3Aauto; timeout 10.000000s
2019-08-12 16:51:28,880 - synapse.http.federation.matrix_federation_agent - 335 - INFO - POST-104458- Fetching https://matrix.org/.well-known/matrix/server
2019-08-12 16:51:28,984 - synapse.http.federation.matrix_federation_agent - 351 - INFO - POST-104458- Error fetching https://matrix.org/.well-known/matrix/server: Non-200 response 404
2019-08-12 16:51:38,894 - synapse.http.matrixfederationclient - 485 - WARNING - POST-104458- {GET-O-3981} [matrix.org] Request failed: GET matrix://matrix.org/_matrix/key/v2/server/ed25519%3Aauto: TimeoutError(10.0, 'Deferred')
2019-08-12 16:51:38,894 - synapse.crypto.keyring - 783 - WARNING - POST-104458- Error looking up keys {'ed25519:auto': 1565621488877} from matrix.org: Failed to connect to remote server
2019-08-12 16:51:38,895 - synapse.federation.transport.server - 286 - WARNING - POST-104458- authenticate_request failed: 401: No key for matrix.org with ids in ['ed25519:auto'] (min_validity 1565621488877)
2019-08-12 16:51:38,895 - synapse.http.server - 79 - INFO - POST-104458- <XForwardedForRequest at 0x7f711034b278 method='POST' uri='/_matrix/federation/v1/get_groups_publicised' clientproto='HTTP/1.0' site=8008> SynapseError: 401 - No key for matrix.org with ids in ['ed25519:auto'] (min_validity 1565621488877)
2019-08-12 16:51:38,896 - synapse.access.http.8008 - 302 - INFO - POST-104458- 2a04:3541:1000:500:6866:a4ff:fe4c:58c1 - 8008 - {None} Processed request: 10.018sec/0.000sec (0.013sec, 0.001sec) (0.000sec/0.001sec/1) 118B 401 "POST /_matrix/federation/v1/get_groups_publicised HTTP/1.0" "Synapse/1.2.1 (b=matrix-org-hotfixes,873ff9522)" [0 dbevts] root@matrix-nitrochat:/etc/matrix-synapse# tail /var/log/matrix-synapse/homeserver.log -n 200

curl matrix.org/_matrix/key/v2/server/ed25519%3Aauto says:

{"old_verify_keys":{},"server_name":"matrix.org","signatures":{"matrix.org":{"ed25519:auto":"IV3Ql81UyFkZdPD9JbdxcqMeKoflQCiR1OgUvumu87tNFa9XC/gNdtcBn2xIYut73KZ1IFZZDvGdlwgdTUxvBw"}},"tls_fingerprints":[{"sha256":"Pq3kW4n2StFnOFtA0PTiXIk0HZF6jwLyR8tMlaRko6I"},{"sha256":"mVNAmfjFleUpJseTNjU5EhJAlfl5rjb7JJPG2UeH9eY"}],"valid_until_ts":1565756981005,"verify_keys":{"ed25519:auto":{"key":"Noi6WqcDj0QmPxCNQqgezwTlBKrfqehY1u2FyWP9uYw"}}}

We run the latest Synapse version on Linux already. Азат at #synapse:matrix.org confirmed it's a Synapse issue. Please help.