I don't know what you mean by the "latest version", and I don't know which exact command you are using, but normally the move and scroll commands are set up to use keyboard emulation. They will only work on the same computer as VoxCommando, on whatever program has focus. Try using the same command on some other program.
In version 0.872 you can change the commands to use xbmc button codes instead, if keyboard emulation doesn't work on your system for some reason. It is not quite as fast as keyboard emulation but is still pretty quick.
Example actions:
XBMC.Btn.KB Up
XBMC.Btn.KB Down
You say the command shows in the VC Window. Which window do you mean?