...There is a rare and intermittant bug with some empegs/installations where the empeg starts up all on its own and the stereo system plays merrily away until the battery voltage drops down to around 10-11 volts, at which time the empeg quits due to low voltage...
Interesting;
A few months ago my Girlfriend's battery died a few times when she'd left her player in the car overnight. She was also seeing intermittent disk errors at the time so I replaced her IDE ribbon. Also, since the battery was a stock 2003 we replaced it. She hasn't experienced any issues since then. She also didn't lose any settings when it happened.

I hadn't equated the two issues till I read your post.
Any way, short of putting some sort of toggle on the +12v lead, to prevent this?