I am dual-booting Linux(Ubuntu 12.04) and windows 7 (SP latest), on an unmodified MSI gx640 with GRUB. Whenever I boot windows on battery power, the next time I try to boot it, it black-screens after "starting windows" and the hard-drive active light turns off.
I can still boot properly in safe mode though, regardless of the power state. The "Boot to last known good boot configuration option usually allows me to boot once I've booted from battery, but usually won't work if I boot again after booting on battery power (getting the black screen), and then try booting from last known good configuration. I have reinstalled both ubuntu and windows 7 multiple times in varying orders, and still get the same problem. Booting from ubuntu always works fine, and I've never encountered any issues on its side.
Edit: The recent power outage we had made me realize that this occurs when it is shut down while on battery power as well. Using it on battery power for a while, then plugging it back in doesn't cause it though.