Transcoding using main audio track only?

Server Version#: 1.13.9.5456

Lately, my recent transcodes have been playing the wrong audio track on clients, including Roku and AppleTV, eg: playing the commentary track. This occurs whether or not Direct Stream is on, or video +/- audio is being transcoded.

Is there any way to transcode files to use ONLY the main or selected audio track?

Any other suggestions?
Thanks!

Which track is numerically first in the file? Commentary or main?
Which track is marked as the Default track?

The first track is main audio, which is also marked as the default track.

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