I've used Get Date/Time in Seconds extensively for timing things. In my experience at least (mainly LV5.1 on Windows 98), it returns the time the OS currently thinks it is, e.g. in Windows the time currently set in the Date/Time control panel. This means that if you change the system time while your VI is running, it will mess up your timings. This is an important point because changes you make in the Date/Time control panel are instantly applied to the system time even though you haven't clicked OK yet!
I don't think there's a problem with the motherboard battery failing though - the PC will start up with the wrong date and time setting but once started it should count up correctly, so relative timings will still be OK.
