With multiple disks you need to go into BIOS and set the disk that you are installing windows onto as first disk in the disk boot priority order. Windows installer puts the files necessary to boot the OS on the MBR of the first disk in the hard disk boot order. This is true even if the first disk is not the disk you are installing windows onto.
This may or may not be all or part of your problem.
Also the term "drives" and "disks" are not one and the same. In windows partitions are named with letters, i.e. C:, D:, E:, etc. But these terms are not necessarily separate hard disks (drives). Example: you can have a single hard disk partitioned with 3 partitions. In windows depending on your hardware setup they will be assigned a letter. For this example I will use C:, F: and G:. These are not "drives" in the literal sense because they all reside on the same hard disk. They are actually partitions on a hard drive (disk). I tend to stay away from calling partitions drives as that is not always the truth. Coming from Linux it is a basic concept and the disk and partition nomenclature makes much more sense. Disks are labeled sda, sdb, sdc,etc. partitions are labled by what disk they are on such as sda1, sda2, sda3, sdb1, sdb2, sdb3, etc. This decreases the misinterpretations of disk and drive and there is no mistaking a partition for a "drive"..