The workaround I posted to https://bugs.launchpad.net/bugs/229851 (now marked as a duplicate of this)
It seems like the ctrl keys use the mapping of the first keyboard in the Keyboard Preferences -> Layouts list. Once I put my primary layout at the top this hasn't been very annoying because I only use key combinations in one layout.
The workaround I posted to https:/ /bugs.launchpad .net/bugs/ 229851 (now marked as a duplicate of this)
It seems like the ctrl keys use the mapping of the first keyboard in the Keyboard Preferences -> Layouts list. Once I put my primary layout at the top this hasn't been very annoying because I only use key combinations in one layout.