I had the same issue with 2 episodes in one file and after trying hundreds of different namings and agent settings, i reverted everything back to where i had it and simply used MKVToolnix and this tutorial here Plex Forum - Splitting Episodes MKV Toolnix Tutorial to split up the episodes into 2 different files. After doing so and naming the 2 new files accordingly, my issue was gone. Unfortunately, this is not solving the main issue here, i understand. But that’s a easy and without much effort doable workaround. If i ever face this issue in future again, i will use MKVToolnix and split them up. Less pain then doing the Plex Dance over and over again and wait for a fix from plex side.
