I have an SE/30 with a recapped motherboard. I've got a new PRAM battery in it and it remains plugged into power. And yet it keeps losing the date / time setting, and the mouse scroll speed setting (i.e. defaults to none of them selected).
As Bolle said. I had a really funky issue on a Classic that I had where cap goo was shorting D2 and causing the settings to be lost and the clock to not even run. Checking all the components supporting the RTC is key.