Now, are you really sure it's the correct date and time? Because if the clock doesn't give a coherent time to the OS on loading, the OS will check the date of the system partition and set the clock to that. If there's no system partition, it will be set to 1978... Maybe it's just the same date and the clock itself is 12 hours out? Big fluke if it is, but try set it a few days in the future and see if it keeps time.
The only other thing I can think of is that you've had some time management utility installed that was malfunctioning (DST utility or something), and copying everything off and back has disabled it...
