Besides draining my battery this can't be very good for the hardware.
Any ideas (besides switching back to Linux) for how to make sure that:
1. Windows turns off when the lid is closed
2. Doesn't somehow start again after being put in the bag.
The reason this doesn't always happen, might be down to Windows Update I presume (or some other application preventing shut-down). Maybe, you can look into changing the configuration/behavior of Windows Update. If it's a "Home" edition, you might not be allowed to turn off automatic updates though...