We have a similar problem, only with Windows Vista and Linux Mint (based on Ubuntu 9.10).
We had Debian Lenny installed on our laptop, along with the original Vista installation, without these problems before. After frustrations with hardware incompatibility, we decided to give Linux Mint a try. This fixed most of the hardware issues. Unfortunately, Vista said something to the effect that recent hardware or software changes has caused problems. We tried the restoring Windows to an earlier restore point option, and that works occasionally, but the problem comes back upon reboot, whether we use Linux in between that time or not. We tried using the system restore disk option. That worked also, but again the problem comes back upon reboot.
So, how exactly do I "rebuild my boot manager"? (simple, step-by-step instructions that don't make assumptions of any preexisting knowledge would be nice.)
Thanks!