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If the server hasn't been shut down, then it is not the CMOS battery, because that battery only matters when power has been shut down.
If time is incorrect, and the system hasn't been shut down ... there's something wrong with your system. Any chance someone with a bad watch is just setting the time and they're arrogant enough to think that "their" watch matters over any else's?
Another possibility (guess on my part) is when the system is running, the time clock is updated by a process in the system. If the server is very overloaded to the point where some processes don't get fair running time, the possibility I'm thinking about is that your system clock is slowed because it has lost some run time during the course of the day.
We have situations with some servers that we know "drift", some are VMs and some are physical.
That's why we make use of ntpd or regular cron runs of ntpdate and point them at a "known" time source, that way all the servers are usually within fractions of seconds of each other.
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