I would edit the OP and add the Plexamp tag, then approach this as that sort of issue by gathering Plexamp logs after rebooting then demonstrating the issue.
It’s a broad topic to speculate without logs, but Elan has mentioned that distorted audio is almost always overdriving a volume setting that goes to 125% of normal or a corrupt Plexamp install.
You get Direct Play when:
- The player supports decoding the video codec
- The player supports decoding the audio codec
- Those two streams are placed into a container the Player can open.
You get Direct Stream when:
- The player supports decoding the video codec
- The player supports decoding the audio codec
- The player can’t open the container. So PMS puts (1) and (2) unchanged into a different container.
When you asked whether Direct Stream could cause this, yes a new container was used, and maybe it’s possible to create a corrupt mkv, but that seems unlikely. MKV containers have been around for decades. Let’s hope it’s not that 
