These have a battery powered RTC/NVRAM chip. If that one starts dying, the settings can go all screwy. And by now, the batteries in these chips are now usually either dead or dying.
I'm not sure because I haven't messed much with these, but a combined RTC/NVRAM implies there isn't another (secret) way the board can store settings.
NOTE: Drilling open the RTC chip to get to the battery contacts somehow destroys it. There seems to be additional circuitry in the epoxy on top of the real chip which disconnects if you disconnect the battery. I had three of these, one was already modded and I modded three and they all give HARDWARE ERROR P11 (or something) followed by a reboot.
There seem to be replacements for this chip though. It's a Dallas part and if you open the card cage, it's in the bottom right on the CPU board, so if you have the additional sound board, it's right under there. Unfortunately it's not socketed.
(Note 2, unimportant - of the two RTCs I drilled open, one had a completely dead battery and the other was at around 2V, should be 3V, not enough to run the clock but still enough to retain the settings, so there is a chance that yours literally just started dying now)