My first reaction is that it is not the "clock" but the mother board's battery. If it were the battery, however, I would expect other symptoms as well since the CMOS would normally have reverted to default settings. But if you hadn't changed any of the BIOS (stored in CMOS) settings you may not notice anything. Changing the battery on the mother board is pretty simple and not expensive.
There isn't a "clock" as such but an interpretation of the time elapsed by measuring the processor "ticks". Setting a time in the control panel is just a user-friendly operation for the convenience of humans. The Operating System really couldn't care less what the "time" is.
The Windows "clock" is separate from the BIOS "clock" too, and they may run at different rates. This reminds me of the government sponsored course I did on the Millennium Bug. Wonder what I did with those notes...
So, I suggest you check and, if necessary, change the battery.