I am stumped. One thing that you could try is when a questionable recording is in progress, go into the TVH WebUI and select the 'Status' tab. Have a look at the stream name and the PID list.
I have been able to recreate the 'Select Program' screen in Kodi on my system, but I needed to do a LOT of trickery.
I did a normal recording.
I also did a full mux recording via VLC.
I then replaced the normal recording file with the full mux file in TVH at the file system level and then when I played the recording in Kodi, I got multiple programs.
This is just a wild guess and I'm not sure how feasible this is, but perhaps your tuner hardware is faulty or your turner firmware is corrupted so that when TVH selects the PIDs that it needs, it gets sent everything anyway.