Keyboard is messed up in Yosemite 10.10.1

I was previously on 10.10 and after fixing the Python problems as described in another thread, Civ IV was working fine. But after upgrading to 10.10.1 the game's detection of the keyboard is all messed up. I have to either hold or press/release CTRL on just about every keyboard command. Grouping units and giving them commands is absolutely infuriating because it's constantly mis-interpreting as if I'd CTRL-clicked when I didn't, or vice versa.

Is anyone else having this problem?

Two years later I figured it out -- this happens when you're set to a different language or layout than U.S.

In my case I was on the 'Romaji' mode of the Japanese keyboard, which types like the U.S. keyboard everywhere but Civ IV