I have seen this happen on many machines, and the cause can be different, but basically you end up with two entries in the boot.ini file which each call for a Windows boot. So when you boot up your computer you are asked to pick which one you want.
To remove this annoyance you can do the following:
1) Right-click My Computer
2) Click Properties from the right-click menu
3) Click the Advanced tab
4) Click the Startup & Recovery Settings button
5) Here you’ll have a choice to choose your default OS. Usually you don’t need to change it as it will already be on the best one.
6) Most likely, the “time to display list of OS’s” will be checked with a timeout equal to the time your computer waits until it boots without user intervention. UNCHECK that box.
7) Reboot and you should boot directly into Widows without the boot prompt.