If your problem is that boot.ini gets deleted every time you reboot Windows, the problem is the recent upgrade to IE8 and the solution is to go into "Add or remove programs" in the Control Panel and remove IE8.
As soon as this was done on my parents' machine, the boot.ini file was left completely alone and it's booted fine ever since.
So well done, Microsoft! You've released a browser that deletes a system file it shouldn't even LOOK at! That's true creativity, that is. Who wouldn't think that a piece of software designed for looking at web pages might be deleting boot files even before it's told to load and run?