Found the issue and have a permanent fix.
I noticed the TV channels with issues were using HE-AAC and the channels that were working were using AAC. Since I’m using xTeve as the back end, I was able to use ffmpeg and force a transcode to AAC for audio and now all my channels are working.
All the credit goes to this guy:: https://www.reddit.com/r/PleX/comments/f0v1cw/2017_nvidia_shield_heaac_audio/