If you are running Windows XP the need for a new installation of Windows is common due to XP's specific "snapshot" process of the total hardware installed on the system it goes onto. This is part of the Microsft intent for one disk for each system. Once you make a major change similar almost to a new build you will have to perform a fresh installation which will delete the current Windows, Program Files, and DocumentsandSettings folders.
You don't always need to reformat the entire drive for this if you are only swapping boards. A repair install allowing for the installation of new drivers for the new board and your current video and sound cards could work there. That will depend on whether or not you are only changing that and not swapping other hardwares(memory, video and sound cards, cpu) along with the board.