I have two HDHomerun Connect tuners and have added both as individual devices in Plex.
I have separate antennas on each device so I can receive different stations from the directional antennas.
In the Plex DVR setup of the devices I have enabled the channels in a mutually exclusive manner so the tuners with the best signal are only used. In my case, only channels 10.1 and 12.1 are enabled on my device at 192.168.1.128 and all the others are enabled on the device at 192.168.1.121 with the exception of 10.1 and 12.1.
The problem is that when I try to view channel 10.1 Plex is trying to stream it from the device at 192.168.1.121 which has it disabled in device setup and fails because there is not sufficient signal.
I have removed both devices and re-added them and the problem still exists.
Using the HDHomerun app on my tablet or HDHomerun setup on the Win7 computer I can watch 10.1 just fine from the 192.168.1.128 device.
Plex just seems to be incorrectly tuning the 10.1 and 12.1 channels.
Have you tried scanning the channels from the HDHR devices and only enabling channels you want used in each device, then scan in Plex.