> When the OS is not running then the CMOS battery is powering the clock and
With respect, you've just repeated the same mistake. The CMOS battery
powers the clock ONLY when:
1/ The external power to the computer is switched off or removed
2/ (In the case of a laptop) the laptop battery is removed
Only then does the little button cell on the mobo take over. Whether the OS
is running or not isn't relevant.
Unfortunately, I can't explain the odd symptoms the OP is experiencing.
However, I seem to think that Windows does NOT use the mobo clock all the
time - I believe it keeps track of time internally. Presumably this is what
is malfunctioning. As damocles says, perhaps a cold boot will sort it out.