I don't use the Channels clients that often, so forgive me if this has been brought up and was solved.
Using the latest release 4.2.0 of the iOS Channels client on my iPad and connected to my Channels DVR server which only has a TVE source enabled (I don't have my HDHR Prime enabled as a source on it).
The iOS client is set to have the TVE source higher priority than my HDHR Prime (which is on the same network and the iOS client sees it).
When I view On Now or Guide and filter Favorite channels it displays the HDHR Prime channel instead of the TVE channel where the favorite channels are the same, for example my local PBS channel is favorited on both TVE and Prime sources.
If I filter ALL or HD channels it displays them both.
Only workaround I've found is to disable the Prime in the iOS client, but then when I connect to my other Channels DVR server which only has the Prime as a source, it doesn't work because the Prime is disabled in the iOS client.