the M2-ATX has a "hardoff" setting that cuts all power (including the +5vSB rail) after a set amount of time.
you can turn the hardoff feature on/off as well as set the hardoff delay time via jumper settings. what jumper setting are you using?
you can see view the full list of possible jumper settings here. you should not use any of the "never" settings, as these will drain your battery. use only the following settings (I use the first setting, and would recommend you do the same as long as your PC shuts down in less than 45 seconds).
although that should stop your PC from draining your battery when your car is off, it still shouldn't have drained your battery in such a short amount of time. it sounds like you have a problems with your car's electrical system. you could have a bad battery, a dying alternator, or another device draining your battery.
ABCD OFFDELAY / HARDOFF
1000 5 seconds / 1 minute
0100 5 seconds / 2 hours
0010 30 seconds / 2 hours
0001 10 minutes / 1 hour
1001 15 minutes / 2 hours
0101 1 hour / 1 hour 15 minutes
1101 5 seconds / 2 hours