This is a long standing known issue that has been investigated for some time. If you would like please send me a PM on this site with the channels included in your favorites list and I can attempt to do some testing to see if I can get more information for you.
I can't speak to why or what an agent may say on the call in regards to this issue. I can say there is a known issues list that is available to all dish network employees and this is issue is on that list. It does include the work around which is to change to the my channels / all subscribed channel list, then change back to the favorites list.
While I cannot state this as gospel, some reports do suggest the issue is tied to having collapsible channels included in your favorites list. An example would be the Big Ten Network which is channel 405-1. So if you have some of those channels that include a dash in your favorites list it may be worth it to try removing them and seeing if the issue goes away.
Our technical operations team are working on getting this resolved. Issues like these require multiple account examples so that they can isolate the problem.
The timeline of the solution will depend on what the issue is exactly and what resolution is needed.