Something like that mostly happened with me having broken memory in my computer (not totally broken, but for example, if I left the computer on for like, half an hour or so, it would jam up and I would have to restart the computer, possibly screwing up Windows in the process, which it did in the end).
So, with all the other tips you've gotten, I recommend you to run a memtest, if you still can. Or if you have spare memory somewhere, try them and see what happens with the Windows boot.