My current computer setup uses Synergy to move between my Ubuntu and Mac OS boxes. This allows me to seamlessly use them both as if they are one computer with only one mouse and keyboard.
The mac is a mac mini and I don't really have space to leave a keyboard plugged in so I leave it unplugged unless Synergy has a problem where I need direct keyboard and mouse access.

This makes the mac complain every time its turned on saying there is no mouse or keyboard plugged in.

To stop your mac from searching for input devices every time it turns on follow these steps

Select System Preferences

Select Bluetooth

Select Advanced

Uncheck "Open Bluetooth Setup Assistant" and select OK

You may also need to disable the keyboard assistant, especially if your also using a KVM.

I am not sure if there is a better way but this has worked for me.

Open a Terminal window and type the following at the prompt

$ cd /System/Library/CoreServices

$ sudo mv KeyboardSetupAssistant.app/ KeyboardSetupAssistant-OFF.app