I ran into this exact same problem today. It turns out that the wrong preferences are shown if you do not have a "PrefsObject" in your channel code (usually this is added to the main menu).
For me the issue occured in the TWiT channel, making sure we always have the PrefsObject makes it work like expected: https://github.com/plexinc-plugins/TWiT.bundle/commit/66e6b9bf31212c0274a255787440eba9c440a360
