Unclear if this is TMH or job queue issue or what.
Sometimes certain video/audio files on upload will have transcode jobs be "queued" (according to [[commons:Special:TimedMediaHandler]]) but they never run until someone presses reset transcode. This only happens rarely, a couple files a day. Most files have their transcodes run fine.
Most recent example is: https://commons.wikimedia.org/wiki/File:Wikimania_HongKong_2013_by_Olaf_Kosinsky_Video_13.ogv I've seen several other examples (gone now as I pressed reset transcodes)