When this happened I was using the Via SP13000 motherboard. I left the car at a shop for an entire week and when they went to start it up, it was dead.
It would survive 3-4 days at the most. Now I'm using the Jetway 1.5GHz board, but have yet to test this and I'm not interested in doing so either :). I have left it over the weekend and it's fine. I don't know what causes this, but it does happen. I'm using the M2-ATX as well. I know it's not supposed to, but it does.
Hibernating itself uses no power at all. All of the RAM contents are written to the hard drive then read back in on the next boot.
The problem could be that some motherboards keep external devices powered constantly. A common one is the keyboard and mouse (this is so that the computer can be started by using a keyboard/mouse button rather than the case button). Have a look at the BIOS and there might be a setting like "Keyboard Power-On" or similar.
Otherwise you might just have to install a timed relay switch which actually cuts power after the car is stopped. Or a flip-switch would do it (except you would have to flip it every time to use the carPC).
Hibernation uses zero power, only standby on PC's requires power. If you are draining your battery down, something else is pulling power. Your pwer supply my not be going to zero drain or something else is staying powered up.