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I think the original WinCE problem stems from the fact it doesn't read the actual RTC again after it boots, it uses an internally ticker interrupt to mark time using the system clock, not the 32.768 KHz. It resyncs when it reboots next.
What's driving your primary clock, some generic crystal, or a TCXO with some reasonable ppm rating? Have you actually calibrated it with a frequency meter a couple of orders more accurate than the level of accuracy you desire?
Calibrate your clocks, and be aware that quartz oscillators age, and are effected by temperature, voltage, etc.
A good comparative source would be a local NTP server, or GPS 1PPS.
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