Check the boot sequence in your BIOS, it sounds like the machine is looking at the wrong hdd when booting. Usual boot sequence is Floppy, the hdd the OS is on, and the DVD/CD Drive. The data hdd shouldn't even be included in the boot sequence. I was helping a friend yesterday with a Dell and had to go into the BIOS and "turn on" both hdds when there were to and "turn off" one when only one hdd was corrected but this was a Dell and had never run into this before.
I swapped over the IDE Cables. So the cable that the hard drive was working on (CD Rom cable) was the one being used for both hard drives....It didnt work.
I dont understand why, I've reconnected it so the hard drive is on the same cable as the CD-ROM (Currently disconnected as the cable is not long enough for both hard drive, and cd-rom to be connected at the same time.)
It still takes as long to boot when the 2nd hard drive is connected.
I thought the outside one (Closest to the edge) should have the CD Drive because...
The inside one is IDE Channel 0 Master/Slave Which i had my hard drive plugged into.
The outside is IDE Channel 1 Master/Slave which i had the CD Drive plugged into.
At the moment the only way the hard drive is working is by having it on the CD-Rom ATA cable.
Is there any concequences of running the master hard drive on one cable. And the Slave hard drive/Master CD-Rom drive on the other cable.
The boot times are extremly long when the other hard drive is plugged in. But i can live with that and move around my cd-rom drive so that the cable can reach if i know if will work properly, without any concequences.
If you have only 2 ATA drives, a hdd and a CD drive, then use a separate cable for each, they should both be set to Cable Select though it's possible they should be set to Master but try Calbe Select first. You can check your mobo manual but I'm pretty sure that the hdd should be connected to he first one and the CD to the 2nd, I think the CD connector is blue. Once you have them on separate cables there will be no Slave unless there is an addition drive on the cable. It's the cable that determines if you have Master Slave not where they're connected on the board
As a test do you have any other computers that you can test the new hard drive on? Its possible the drive is bad and the bios is just taking a long time to see it.
Have you formated the drive yet/used it?
Having hard drives on seperate cables wont hurt anything at all. In fact any transfers from one drive to the other will be a little faster since they are on seprate channels.