Windows doesn't know it's running on a Mac.
BTW When you say GTX 260 do you mean the Radeon 2600 series as I cannot find the one you mention by searching their web site. The only cards that work in the Mac running Windows are the ones specifically designed for the Mac such as the 8800GT or the HD3870. Just because you're running Windows doesn't mean you can install any video card. As far as the other cards are concerned, as long as they are compatible with the PCI Express bus you're good to go.
I don't want to get too technical but there is one exception. You can have a Mac compatible video card in Slot 1 and a Windows only compatible card in slot 2 (as long as you do not exceed the maximum power requirements of the PCI Express bus) so when you boot to Windows it will be recognized. The only problem is that you will have to switch your video cable from one to the other.
Having said all of that order your MP with the 8800GT and get Vista 64 and you will be happy.
BTW If you intend to do gaming, you can install a SoundBlaster PCI Express XFi sound card. It will not be recognized by OSX but Windows will see it and use it (great card as the MP doesn't support Dolby Digital in games - not sure about professional apps so check other forums here first ).