I had a similar issue, and a complete reinstall (Win 10 instead of Win 7) + completely new install of latest Plex Server + Desktop Player seemed to fix the EAC3 5.1 issue. But I’m not certain whether it was the Win 10 part or the fresh install of the software that did the trick.
You can check my thread here:
There’s also a log file at the top, for anyone who wants to compare notes. There are codec errors in that as well. And no special permissions were set/disabled for writing to any temp dir on my Win 7 setup (no permission I could detect checking the folder properties, at least).