I have hundreds of video assets, and this problem just started this week. I encoded a new series with 30 episodes. They are all h264 in 1080p, AAC 2.0. Only a handful show up in Plex as 1080p 20 Mb. The rest show 720p 4 Mb. This is in the quality pull down menu.
I tried running "optimize" for "original quality" on one of the bad ones, but that made no difference.
In the info page they definitely say 1080p.
They were all encode with Vidcoder at high profile, the same way.