Comment #19 on issue 1558 by [email protected]: Ibus 1.5 does not effect 'use system layout'.
http://code.google.com/p/ibus/issues/detail?id=1558
If you look in the Anthy preferences under ibus (the button's in the place where you can change the order of the input methods), you can adjust the layout used with Anthy. I chose the 'system layout' (not to be confused with the global 'system layout' in ibus) and got Dvorak.
Also, setting XKB options via setxkbmap solved all of my issues regarding caps lock and compose.
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