No, not new. The client apps have always combined the same channel from different sources into a single guide entry. (On the other hand, the web UI for the DVR server never combines channels; each is always individually listed.)
My recommendation: keep the TVE channels marked as a Favorite, but do not mark the same channel as a Favorite for your OTA source. That way, if you select the channel from the All, HD, etc., listing in the guide, you will get the OTA version. If you select the channel from the On Now or Favorites listing in the guide, you get the OTA version.
Also, you can still directly tune the hidden channel with number entry (if using a remote), or by using the channel +/- keys on your remote. (Also, if you keep your Guide set to All, the Quick Guide set to Favorites, and Channel Surfing set to All, I feel you'll get the maximum flexibility.)
Remember: priorities and favorites are per client, and separate from the DVR. Client lists of favorites and priorities are solely for tuning/watching live TV; the DVR's priority and favorite lists are used solely for determining which source/channel to use for recording.