Comment 8 for bug 273299

After more aggregate experience, I can confirm that plugging in or unplugging an Apple USB keyboard seems to cause or aggravate the issue. Often the applet doesn't crash, but rather shows a default configuration (only one option: USA) and both builtin and external keyboards are left in qwerty. On occasion, unplugging the Apple keyboard actually makes the builtin keyboard return to Dvorak (!). (Or maybe the internal keyboard had just stayed in Dvorak and I hadn't noticed.)

This is all very strange. I could probably be of more help tracking this down if I knew how all the keyboard layout stuff worked. I haven't found much good documentation about it beyond xmodmap.