Note which version of Plex and OS you're using and obviously check their discussion forums, but I seem to recall over the years several DTS & Plex related bugs which caused just what you're hearing--surround in the wrong channels, i.e. center channel NOT being sent to the center channel speaker, but with 'DTS' seemingly properly registering on your AVR. Maybe 3 years ago was when I switched to XBMC exclusively, and XBMC never had that bug because they upgraded the video and audio underpinnings more quickly than the Plex team did. I forgot offhand what the resolution was, whether you had to remap the surround output channels in AudioMIDI, whether it was a bug in Handbrake that only affected Plex, so do check over at their forum. You can confirm it is a Plex only issue by seeing if you get the correct audio where it should be in VLC and XBMC.
I always keep an aTV/iOS device Handbrake transcode of my movies just the way Apple wants you to do it: AAC audio first, AC3/DTS passthrough second. That's in addition to the full-size MakeMKV rip for the Macs in the HT.