If your system is running ntpd (Network Time Protocol Daemon), this could readily happen. NTP is a protocol that permits an operating system to work out the "one true time" by consulting with other machines. If your hardware clock is not precisely calibrated, its notion of time will diverge from this "one true time" that is retrieved from the 'Net.
The hardware clock is only changed when the system shuts down. On restart, the system initially takes its idea of the correct time from the hardware clock, but then, once ntpd synchronizes with other systems on the net, it begins to correct the local time of day to bring it into agreement with the consensus value.
To make a long story short, if you are running ntpd, do not worry about the divergence of the two clocks; the OS will keep more accurate time than your PC hardware, which will only be used as a backup in case the network time is not available for some reason.
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