The thing is, all a boot sector is is some things that get loaded into RAM quickly on startup so that Windows can load. It's not something that Windows makes changes to often, it basically just reads it. Boot Sector Viruses on the other hand are a much more common thing.
Not saying Windows is ironclad by any means. However, it would be pretty hard for it to corrupt something that only gets loaded into RAM and read once and then basically ignored. If changes are made to the boot sector, it's much more likely that you or a virus did it than Windows.