Hi,
You can choose to only share keyboard if you're mirroring input across multiple machines. When using Input Director to control a set of machines individually, mouse&keyboard are shared together.
If mouse actions are being duplicated as there is a game running on the director system, then there isn't much that can be done as games will often hook into mouse/keyboard input in a different (low level) way that standard applications, which can't be trapped by Input Director.
Regs,
Shane.