mojjj: The Chili Docking widget is only needed for saving window sizes and positions. Things like which widgets are enabled/disabled should be saved no matter what, although I'm not sure where they get saved to.
Like KR says, it could be a permissions issue, or maybe the save location has been accidentally set to someplace that can't be written to (like a CD drive or something).
Or maybe Arekow is pressing one of the "settings" buttons in the Lobby? They're labeled "Game details" and mostly deal with graphics settings, but they also reset some widgets (but not all of them).