Not really sure what you mean. As you know you have your DVR Sources that have a particular order. My OTA is last since it only has those channels not used by any of my other Sources.
TVE Channels "only" show up in TVE Login Sources. Not with HDHomerun's.
On your client you also have all of the Sources and each client can have it's own Source order.
Anyway, I have 2 DVR's and 8 Apple TV's (seldom use my iPad's or iPhones for this but have in the past). I have not problems getting everything on all of my clients. I add my source order the same for all of my clients but that is my choice. If you are using a client with the NEW SORT ORDER maybe you are using NAME ORDER instead of Channel Number Order which would mean it is under LA-KTLA5 for now.