Subtitles Causing Playback to Glitch Out

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Your transcode log is essentially empty. With the remux log there's timestamp errors on a regular basis as well as some invalid data warnings. The former shouldn't cause issues, the latter will definitely cause issues.

You are correct -- subtitle extract ignores PGS/VOB titles because extracting them does no good -- only SRT subs are extracted. With OpenSubtitles, some subs will not match your media. You can change the alignment via settings in most clients.