260 GTX - Windows won't shutdown properly

Fresh install or was it working properly before you replaced the card with the 260GTX? I have had some extended shut down times after swapping some hardware before. I generally just let the machine shut down on its own time on initial install and restart. After the device is installed properly the shutdown times go back to normal. Is the device trying to reinstall every time you start the machine up? If so I would let the device install and then restart taking however long the machine wants to complete the shut down process. If its properly installed and not asking to reinstall each time the machine boots then I would put the original piece back in if it was replaced and see if the machine behaves normally again. If this is a fresh build then I would get a replacement card and see if the system still acts up on shutdown.