CMOS clock drift - Suse 9.0

Hi, I have Asus Pundit with Suse 9.0 and just cannot get cmos clock to be right across reboots. I'm not yet sure whether boot is messing clock, but still would like to ask what is "Setting CMOS clock" on boot doing and why does it take so long to do it? Can this somehow mess with my clock ? I've just replaced CMOS battery, so this cause should be excluded.... Regards, Robert.