This is easy to reproduce now.
http://try.discourse.org/t/open-links-in-external-window-test/344
It is because the first two links are using protocol agnostic URLs, they do not start with http: or https: and instead start with //
try.discourse.org is temporary, so here is the code to reproduce the issue
[MusicBrainz's community](//community.metabrainz.org/t/do-i-have-to-hit-the-save-button-after-scanning-music-in-picard/20489/3?u=jesus2099) - won't open in new window.
[Discourse 1.6.0.beta1](//github.com/discourse/discourse/commit/1481b3420ec1fa8514a9f37ec8947d91b9642731) - won't open in a new window
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[MusicBrainz's community](https://community.metabrainz.org/t/do-i-have-to-hit-the-save-button-after-scanning-music-in-picard/20489/3?u=jesus2099) - will open in new window.
[Discourse 1.6.0.beta1](https://github.com/discourse/discourse/commit/1481b3420ec1fa8514a9f37ec8947d91b9642731) - will open in a new window