Finally discovered the source of my phantom DNS issues at home. Turns out my OpenWRT AP, which used to be my router previously (and still terminates PPPoE) still had a daemon sending out router advertisements with DNSSD on link-local IPv6 (fe80::X), dnsmasq forwarding to 8.8.8.8.
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So global DNS worked fine, but my internal stuff (LAN domain and some stuff I forward for staging/testing environments) would randomly fail to resolve or resolve to the wrong IP via public nameservers (for some it's split DNS) when the query got sent to the OpenWRT box.
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And of course, since positive replies get cached by the local dnsmasq (managed by NetworkManager), it would usually work on the second try and stick for a while so it wasn't *too* obvious.
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I think this started when I turned that feature on (needed for split DNS with VPNs), because IIRC by default dnsmasq has different behavior from the system resolver (round robin / random instead of trying in order) - previously rogue would probably wind up third and get no hits.
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I should document my home networking setup sometime. Physically it's super simple (VDSL modem, Netgear router/AP, extra switch, 4 computers and some game consoles) but logically there's 9 VLANs, 7 SSIDs, 3 network namespaces, multiple VPNs, IPSec between some hosts, ...
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