An Update: after getting a complete copy of the system that my customer is having the issues with I find that even when the unit has 'stay off after power failure' settings the unit will not power/initialize the usb keyboard and trackball from an unpowered state (disconnected for over 1hour). If the unit is powered off (not disconnected from power just shut down) then restarted it will detect them. My customer is asking me to look into another motherboard manufacturer if we dont get to the bottom/cause of this.
I found a similar problem with an Intel DP55WG motherboard using the HP keyboard (USB) with Windows 7 64-bit.
The problem was "triggered" when the LEGACY USB support was activated (turned ON) in the motherboard BIOS.
Problem disappeared by keeping LEGACY USB - OFF.