I'm assuming you're running Windows 2000 or XP.
Boot from the Windows install CD, and when the first menu comes up, select the recovery console. On the black screen, select the number for your windows installation (usually 1) and press enter. Type your login password, if you have one, and press enter. At the prompt, type "fixboot c:" assuming c: is the drive that your operating system is installed on. Press Y if it asks you to confirm, and when it gives you a prompt again, take out the cd and restart the system. That should fix your problem.