This is a recurring bug that Ive noticed pop up here and there on the forums. It hasn't been addressed either because its low priority or because no one knows how to fix it. When your in game and decide to switch toons or are logged out due to inactivity the game defaults back to a native login screen which does NOT use the reg files for StarTrekOnline as its resource.
Mine defaults back to my old Cryptic Login instead of my new PWE login, This looks like its not reading the SQL tables on the remote server correctly or that its read the old ones. Somehow though this is an annoying bug that I know has been around since february.