Control not working in iTerm 2 when using Programmer Dvorak keyboard layout

I'm using the Programmer Dvorak keyboard layout and found that the Control key does not work in iTerm 2. Emacs is unusable as a result, and I can't interrupt processes with Ctrl-C. Interestingly, the only thing I have found control to do is that Ctrl-Z still sends SIGTSTP. I've swapped the Ctrl and Caps-Lock keys at the Mac level, but undoing that has no effect. I use zsh, but running bash doesn't help. Everything works fine in Terminal. How can I get a working control key? PS: Reverting back to QWERTY does fix this, but that's not really an option.