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I think my problem with the subtitles is I didn't find and uncheck all the 'forced only' subtitles boxes, but two of the episodes on this Blu-ray disc have commentary tracks and I want my ripped versions of the episodes not to have them. Which audio boxes do I uncheck to make that happen?

If you don't want any extra streams in the file, other than the video and main audio, then you can right click and select 'Unselect All' then select the main audio stream. The right clicking thing isn't recursive, so you'll want to unselect all the forced sub options.

SC