I imagine the RTC circuit was not properly oscillating with the faulty battery. Here's what happens under normal circumstances:
- RTC oscillates normally while system is on.
- When main power is cut (system turned off), the RTC circuit automatically switches over to use the battery backup. This is done using logic that is built into the circuit when the input voltage falls below a certain threshold.
- RTC continues to oscillate normally while the system is off -- using the coin battery.
- When the main power returns (system is turned on), the RTC circuit automatically switches over to use the main power. This is done using logic that is built into the circuit when the input voltage rises above a certain threshold.
Note, the point I'm making here is that the RTC circuit operation is completely self-contained under normal circumstances. It requires no input from the BIOS and will hum along on its own generating ticks with the system on or off without intervention. Now what happens if the battery dies? Tje RTC circuit shuts off when the system is powered down. This means that when the system is turned on the RTC circuit is in an abnormally shutoff state and possibly needs to be reconfigured to restart it. Some RTC circuits require "jump starting" by pulling some of their lines up and then down abruptly. Perhaps, the BIOS wasn't restarting the logic because a bios "reset" hadn't occurred. On older systems the loss of a battery would result in the VRAM settings being killed so a restart of the RTC would always have been triggered then. In this case not necessarily so. Now, I don't know for sure if that that is what was happening, but the fact that your clock was not ticking in the BIOS suggests that the RTC is not oscillating. And as for within the OS, your RTC circuit does not necessarily need to be ticking to keep time there. There are other clock sources such as HPET and TSC to keep time with.
I have a similar problem. New machine, keeps time only when not asleep. As soon as it goes to sleep, the clock stops. I changed the CMOS battery already - no change. I looked at "time" from the command prompt and it is in sync with the clock in the taskbar - both wrong. Windows 8, Gateway computer SX2865. Can anyone tell me what to do next to troubleshoot?
I'm assuming the RTC circuit is not functioning correctly. You may be able to run diagnostic on the machine to see if it detects whether it is working (some machines have built in diagnostics). Try resetting your bios and also try clearing the settings via the jumper instead of the bios utility to see if you can "jump start" the RTC circuit. The circuit itself could simply be faulty. It may be ticking just fine during normal system operation (or it could be something like I wrote above), who knows.
Whenever I had RTC circuit issues in an old dell laptop, it would just warn me during the initial post and I'd pull the battery to get it working again.