this is actually the same problem i'm having with knoppix or ubuntu. after install i can't boot em cause grub doesn't know of the controller. Only way it works is for me to connect them to an slow ata33 bus. which makes my comp extremely slow.

I can install it cause the knoppic CD has the drivers but once its installed there is no way for me to boot it.
So its not just windows, its any OS installed under my ata100 controller.