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I have a weird situation, because I use a custom layout [similar to Dvorak]. Sometimes apps respond to the key as though it is what's labelled on the keyboard, rather than what's mapped... e.g. Dvorak's V is on QWERTY's ., and when I press Ctrl+that now, I get <sup></sup> rather than paste.

The keyboard layout is configured using the old Xorg crap. The best solution is probably switching to keyd and letting Xorg die away quietly.