Just FYI: I am running the most recent Keyclone (1.6b? it's at home so I can't say for sure, but I update very frequently) and all my keybinds are ctrl-# or alt-# and they work fine.

I did have a problem a while back when you added the "differentiate left/right" but I think that was because I'm using G-Keys to simulate ctrl-# combo's.