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I ripped a episode from a DVD and it plays okay on the Plex Web App, but using the Plex app on my Roku the audio is really low overall and fluctuates in volume. I tried only including the main audio track with the same result.

Any thoughts regarding the issue are appreciated.

Most likely, Plex is converting the AC3 audio to AAC for "compatibility", which usually results in a 3db volume loss when the AC3 uses Dynamic Range Control.