Have you actually let it run all the way through, when it's booting up, by the way? It's possible that something happened in Windows that triggered it needing a DiskCheck on bootup, and every time you cancel it, it reschedules it for the next time you bootup (my laptop does it every 30 boot-ups, but the Linux version takes nowhere near as long as the Windows version).

Of course, if you have let it run through once, and it's still doing it, ignore everything I said above!