Typically at startup the operating system (read windows) sets the system clock to the RTC. After that the operating system generates interrupts(depending on the flavor of windows it could range from 10 ms to 15 ms or more) to update the system clock. Also if Windows finds the time lag between the two clocks to be at least 1 minute (Where exactly this value is set is not known publicly!!!), then it resets the system clock to the RTC. But if you want to keep up the system time much more accurately (say 100 ms, then there is no way to do that.
ClockMon is a simple utility app that can be used to monitor the two clocks or resync the system clock when it drifts away from the RTC. It is a free program that can come quite handy when troubleshooting clock drift issues in applications running on Windows platforms.