I think both of the games are required to be in the forground to work.

I haven't tested this, but I think Keyclone can set the slave windows to be flagged as in the forground.
That being said, the only way I got CoX to work was two-boxing it on 2 PC, and I ended up using Hotkeynet to do it as that was the only software I could find that mentioned how to do it. :P