I realize I am a little late on this one but I was having the same issue. The fix is to ensure Keyclone doesn't have any compatibility mode selected. I.E. Run this program in compatibility for XP SP2 or Win2k etc. Vista opens a separate window for the sound driver and keyclone focuses that instead.

So for anyone searching this problem there is your fix. For your clones just add the -nosound switch to the command editor.