After the 10.2.4 upgrade I'd been experiencing the same kind of wonky keyboard layout preference issues that several others have reported. After a restart and auto-login as User/Admin my preferences were reset to U.S. default but enabled Canadian CSA, which I mistakenly enabled during my initial 10.1 configuration in August. And while earlier 10.2 versions would remember that I turned off the Canadian CSA layout while logged in as User/Admin, 10.2.4 did not.
So after seeing a MacFixIt forum thread ( from Jan 20 2001! ) on a similar issue - I tried the suggested fix of logging in as root, resetting the input options in the System Preferences International pane and restarting. So far - no problem and no more flags in the Menu bar.
Hope this isn't old news and that other folks can address their 10.2.4 keyboard weirdness this way.
Joel 02QuickSilver 933/512 10.2.4