|It sounds like the Secondary IDE controller is disabled in the BIOS.|
If you have TWO drive connected to ONE cable they must work together. Either both must be jumpered as CS (cable Select), in which case the end connector will be the master drive. Or make one Master and one Slave, in which case it doesn't matter which connector you use, the master will be the master and so on.
If I understand you correctly, you now have 3 drives. If all are connected using the wide ribbon cables then one of the drives is ALONE on one of the channels. There are a couple of things to note in this case. First, the Secondary IDE channel must be enabled in the BIOS screens. That is usually located on the second or third screen.
Second, if you have a Western Digital Hard drive and it is connected by itself there is a special jumper setting for Master Alone.
Best to make the boot drive the Primary Master and then install the other two drives on the Secondary channel.