My problem was that the auto installer was installing grub on the windows drive. When windows was shutting down it f'd up grub.

Installing ubuntu with just the linux drive connected, it installed grub on that drive instead of the windows drive. Now windows cant f with it. I set the bios to go to hd1(linux) instead of hd0(win) by default. As michaaa62 said grub picked up the windows install and added it. I then modified grub with the startup manager to change windows to the default os.