From your description, it sounds like this happens every time you boot.
- Do you only boot your system by switching on the AC power to it?
- Does this also occur after you power down from the OS or by pressing your power button for > 4 seconds causing the system to go into "Soft Off" or ACPI S5 mode?
- Is the time reset each time you have invalid CMOS checksum?
The reason I'm asking is because the VBAT power connection is typically powered by an on board regulator when the system is plugged in and by the battery when the system is disconnected from the AC outlet. You can measure the VBAT voltage and if it is ~3V or less then it is running off the battery, but if it is closer to 3.3V, then it is powered by the 3.3V DC-DC regulator on the motherboard.
If #1 above is the case, then it is likely the battery connection. #2 is more cause for concern that the motherboard isn't behaving as designed.
There is a third potential problem. Some motherboards have a Clear CMOS input which does not GND the path from the battery to the VBAT power input. Instead, when asserted, it clears the CMOS, but not the time. Look for a header with this connection to make sure it isn't shorted.
Also, bad electrolytic capacitors being the cause is unlikely because the VBAT connection is a low current connection and any capacitors on it are not likely to be electrolytic. The 3.3V voltage rail may have capacitors, but even if the voltage dipped, the VBAT power usually can go as low as 2.6V without CMOS corruption.