This is more of a general question than an issue report
Is there any specific factors/thresholds that would cause audio to transcode to mp3?
Most of my media is direct mkv copies of physical discs with the original audio tracks in tact - The only changes i've made is setting the CRF factor of the x264 encoder to a lower value and setting de-interlacing to "bop & weave" , for testing
Update - Added logs
ffmpeg transcode - 10-13-2017 (1252pm).txt
ffmpeg transcode - 10-13-2017 (1254pm).txt
ffmpeg transcode - 10-13-2017 (1258pm).txt