It's very weird. I pushed a change then I went to the channel store and exited and that worked fine. I realized I made a mistake and then republished a package but this one never gets picked up. I have even tried changing the channel/version combination and remove channel and re-added and still the old one persists.
I don't know if this is what you experienced, but you should be aware that currently when you publish a private channel update, it can take up to an hour for the change to be available for download. This delay will be removed in an upcoming release of the Channel Store backend software.
I have usually seen almost instant update, but in this case it didn't . Everything seems to be fine right now, and maybe it was just a weird hiccup. I will remember that about the manifest and make sure to do that.