Comment 1 for bug 161889

This issue is caused by the way you boot Ubuntu. When you select to boot from your second hard disk in the bios, the drive numbers for the first and second had disk are swapped. So while your Ubuntu hard disk is hd1 during installation, it becomes hd0 when you boot from that disk.
You could prevent this problem by installing grub on your first (windows) hard disk. Grub would then give you a menu to boot either Windows (on the first disk) or Ubuntu (on the second disk), and you would not need to change the boot order in the bios anymore.

If you have further questions on this issue, the support tracker https://answers.launchpad.net/ubuntu is probably a better place to get good answers.