Quoted from jlbintn:update, left the game off for approximately two hours, unplugged for the last half of that. All settings lost. And the junk in the registers was back.
I ordered the NVRAM for this game and for LOTR.
While NVRAM is 100% the way to go, if you are still curious what's happening you can make three checks. You should check to see what the battery voltage is at the board. Preferably at the actual 6116 ram but you could sub just checking where the 2 wires from your remote battery pack are soldered. Check with power on, right after turning power off, and then after you have waited long enough that you think it has failed.
With new batteries, it should always measure at least 4 volts (very close to 5 with power on). It sounds like it is dropping below 2V (which is the typical minimum standby voltage required by most CMOS rams) after being off for an extended period of time. Your board might even have a non-low power RAM chip that might not even hold data at lower voltage values.