Welcome to the Windows 7 forum! When the setup file copying process was complete with a second drive added internally by chance? the boot order may have been changed.
The installer would have placed the MBR entries and BCD edit into the original 7000 build's own BCD file while the boot order is set to load from the drive you added in with nothing seen there. You will need to take a quick look in the bios setup to see which drive is set as default there.
If you set the optical drive as first you may want to see that restored to hard drive first and disable the rest to then see the installation completed.