The ctrl- combinations are all taken from the first layout. It seems to be this 
issue, can you confirm this?
https://bugs.launchpad.net/ubuntu/+source/gnome-terminal/+bug/204202

In dvorak the physical x-button will give you a q. So if your first
layout is dvorak and you press ctrl + physical-x-button, you will send a
ctrl-q, even if your second layout is qwerty or something else. This is
independent on what layout you actually are using at the time of the key
press.

I'm not sure whether this is the issue here, since it is unclear to me
whether dvorak is the first or second layout and whether you press the
physical x button, or the button that is supposed to be x according to
the used layout.

-- 
X-Chat is killed by Ctrl+X after changing Keyboard Layout
https://bugs.launchpad.net/bugs/75841
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