Transcoding UK freeview recordings

I’m recording with Plex using an HD Homerun connect tuner.
Everything I record, when playing back on my nvidia shield is getting transcoded.
The information shows the video as direct, but the audio is transcoded with the following message:

Reason: codec (aac_latm) not supported in container (mkv)

The shield is going through a Marantz SR7009 amp. Is there anything I can do to stop the transcoding?
The speed of skipping through ads etc makes it pretty much unusable.
I had one recording with no sound (I think one of the previous PMS builds) and I was amazed how quick searching was in comparison to what I’m usually seeing.