All I can suggest is that you run Boot Repair again and do as I suggest and direct the boot-loader installer to /sda (which should be where the Windows boot-loader is)!.
Another suggestion just hit me, you can swap the drives around, I assume that you currently have 2 HDDās (is that correct?), open the PC casing and make the first drive inot the slave and the 2nd drive into master, that way the drive with your Ubuntu install will become /sda and the one with your Windows install will become /sdb.
If they are older IDE drives, you need to swap the master jumper on the drives around, make the current master a slave and the current slave into the master!.