Never mind, updating to 1.2.3-790-g88a6300 fixed it.
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https://bugs.launchpad.net/bugs/1379436
Title:
Clementine randomly skips tracks on automatic track change
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Public bug reported:
Since the last update, Clementine randomly skips 1 or 2 tracks when just
leaving the playlist alone up to automatic track change. Also, sometimes
it skips several minutes of the following track almost up to the end by
itself. Also, it randomly scrobbles tracks on last.fm when
