I have an Hp Pavilion with a custom hard drive. the hard drive was not the one it came with and it is a western digital caiviar. The problem is that everytime i put the disc in the cd optical drive it would just read it and spit it out. It seems like i have to have a war against my maching. What can possibly be happening.

Your post isn't worded clearly. First you talk about a hard disk drive. Then you talk about putting a disk into it. This implies that you are talking about a removable disk. The WD Caviars are not removable medium drives so I do not know how a WD Caviar has anything to do with some removable medium being spat out of a drive.

The only thing that I can think of given the information in your post is that you have installed a PATA hard drive and the DVD drive doesn't play nicely with it. If you put the WD Caviar drive on the same disk cable as the DVD drive then you may have set the jumper on the WD drive incorrectly when you installed it.

Please clarify your question by adding information about what drives you are talking about and how they are connected to the motherboard and the brands and model names.

If the jumpers are wrong, then one of the drives must not get recognized by the bios in the first place. Is it not the default behaviour?

No. I've never seen the BIOS fail to recognize an IDE device due to incorrect jumper settings. However I have seen IDE devices fail to work properly due to incorrect jumper settings.