Ctrl-key disabled in iTerm.app

I'm trying to use the new iTerm app on my Snow Leopard Mac, but my Ctrl seems to be completely dead (as in non-responsive, as in nothing happens when I type Ctrl+a except for an outputed 'a') and I haven't found anything useful while googling. The closes match was this thread here on stackoverflow, but everything in Terminal.app works as it should.

And, even more strange - I can Ctrl+z myself out of applications, but I can't save files in Emacs (C-x C-s) or any other keyboard shortcuts that uses a Ctrl shortcut. And it's not local, since Ctrl is as broken on my iMac as it is on other unix computers I've sshed onto with iTerm. I've tried both in bash and zsh.

I've tried to remove all files concerning iTerm.app in my ~/Library/Application Support, and I've tried the very latest version (currently 13 h old) of iTerm I could lay my hands on, but to no avail.

Any ideas?