Hey Niceguy.. You have two identical drive. I guess that they are on SATA1 and SATA2 on the primary SATA controller. I would make sure that windows is installed on drive on first SATA controller on primary controller and I woule try to put the other drive on the secondary controller, on SATA1 too. Then make sure that BIOS boot sequence is HDD and you should have another option to select the boot drive. Choose the one that you have on connector 1 on primary SATA controller.
What might have happened, is that first you had windows installed on one drive and that drive is still bootable. Then you manage to install Windows on the other HDD, making 2 bootable HDD, but only one with the NT loader (NTLDR). When booting, maybe sometime it catches the one that doesnt have windows on, but it is still marked as bootable.
To check if that could be the problem, unplug the drive that have windows on and boot. You will see the message NTLDR missing. Now unplug the drive that doenst have windows on, and plug the one that has windows on. It should boot everytime. If not, you'll have to reinstall windows on that drive with the other one unplugged.
If you dont have any important data on the other disk, and want to get rid of the active bit that make the other drive as bootable,unplug your boot drive and in windows install, just delete the partition, and recreate it. And stop the installation. Now, plug back your boot drive and once in Windows, reformat it