I remember when I first added and booted with BIOS, I wasn't using native controller, just wiimote, and got stuck at first boot in gamecube bios, as it asked me to set time and I was unable to do that until I plugged in gamecube controller. So there is a chance that I set time incorrectly and difference is stored somewhere as "bias" and added as "if(CONF_GetCounterBias(&bias) >= 0)" ?
I think the bias is just for timezones. RTCs are generally universal time. Unless maybe it's adding/subtracting too many hours?