I'm assuming you do not use the Brainstem and/or have it with it's own 5v power source (AFAIK the only way to make it work reliably, though I haven't tested it myself yet).
I would first think the same thing, low voltage. Make sure you test voltage at the dsatx, not at the distribution block or on the battery, sometimes the cables/connectors on the DSATX are giving away.
Have you checked the low temp threshold, if it's not turning off due to low temperatures overnight? You could change that. According to this, the operating temp minumun is -40C, but the "allowable" temp is only -10C. I'm in CA, so I've never been below -10C, but depending where you live...check the DSATX setting with the brainstem to make sure.
Finally, have you tried a "hard reset", i.e. pulling the 12v and ground wires and then connecting it back? Maybe it's a software error, I don't know. I've seen stranger behavior cured by just doing the "hard" reset (as opposed to just shorting the reset pins).