|I would guess you just have the cabling/ jumpers configured wrong.|
Your original post indicates you may be using TWO IDE cables to connect your drives (hard/optical). If this is the case then be aware that you have TWO IDE controllers. Each controller can configure TWO drives. So treat each controller separately.
Most OEM computer manufacturers prefer to use CS (cable select) instead of Master & Slave settings. The rule is this: CS settings must be used on both devices on the same cable if used. The device at the end of the cable will be the Master drive. When using Master/ Slave settings the drives may be connected to either connector on the cable.
If you made changes in the BIOS screens you may have some other issue there.
If possible connect the newly introduced hard drive on the secondary IDE controller (primary is usually colored blue on motherboard).
If you managed to boot completely in Windows then the boot.ini file may have been altered and that is the problem.