We identified this issue a while ago and have an internal ticket covering it. We expect to see an updated firmware soon to address it.
Jessy
Apparently when we added the Web GUI override the config files it truly is Web GUI only changes. It does not cover LCD Menu changes. We are adding this in the next firmware and changing the name of that option to be User Override Config files so it will cover both Web GUI and Phone LCD changes.
Awesome Guys!! Thank you. 