update
Upon further testing, it would appear since the latest Plex server update and the PS4 client update. The PS4 Plex app upon boot instantly drops the PS4 from outputting digital surround, be it Dolby or DTS down to Prologic.
Everything from AC3, right upto DTSHD-MA now simply plays in lossy prologic. My server and PS4 played and streamed the corret audio fine before the updates.
