Windows XP boot question.

Hello,
I updated my dads Windows ME to Windows XP and about a week later it started running scandisk everytime he starts up. He is complaining because he has a 10 sec interval where i can choose to skip it and if he don't then it seems to take forever. We are shutting down the computer properly but for some reason it isn't registering it being done right or something. I was just wondering if anyone could give me some information on how to remove this from his computer. Thanks
Steve