Windows has always tended to mess up the bootloader if there is more then one drive plugged in while installing.
It will split the bootloader between the windows drive and another random drive of its choice. Making sure the OS drive is first in bios boot order and in SATA/IDE port number is irrelevant here, windows does what it feels like and messes it up.
This causes issues if you remove the secondary drive, but also if you change drive order around, etc.
The only safe way to install windows is to only have the OS drive plugged in. This forces windows to put all components of the bootloader on that one drive which is then mobile (you can move it to another computer and as long as you select it as the boot drive from the bios it will boot up that windows instance)
It's not hard at all, in fact that's what I did last time but this time around it just slipped my mind and I kinda thought, uhhhh shit am I now going to have something go wrong? Everything has been fine though.
If you already installed it, here is what you should do, unplug all drives except OS Drive and turn on PC. If windows loads then you lucked out and it put all components of the bootloader on the OS drive. If it fails to boot then it split them up and just keep in mind that you will have issues if you swap drives around.
That being said, there is hardly a reason to waste your time fixing it now, just fix it if it becomes an issue in the future.