Set the BIOS boot priority to boot off the second hard drive as suggested. When ubuntu boots up, open a terminal window and type
and see if the OS prober finds the Windows and insert it into the grub boot menu. If it does not, then you may have to repair the windows boot files. It looks like the installer may have tried to put the grub files on the first hard drive.
If you haven't already done so, I'd recommend booting Ubuntu and mounting the first hard drive, then backup any and all important data to something safe, such as an external hard drive.