TV Show MKV - Audio Stream Changes from 2.0 to 5.1

I have many MKVs that are reported as having a single stereo 2.0 stream. However, when playing the audio will automatically switch to a 5.1 stream (generally following the opening previews).

I am trying to remux the MKVs to M4Vs. However, I can only seem to capture the 2.0 audio.

I've even tried re-encoding the file using Handbrake, starting at a point after the audio changeover.

Any ideas on how to remux and use the 5.1 portion?

Thanks in advance.