I've had this exact problem a whole lot, always with WD hard drives. One thing to try, there is a jumper that specifies Master, Slave, or Cable Select. Remove it completely. It will then recognize that drive as the master. Is it on it's own ATA cable? If so, you could try jumpering it as the Slave if it's Master (or vice versa). If it's not on it's own cable, try putting it on it's own cable.
If any of this works, then get a new drive and back that stuff up, because it wont last. I've had so much agita with WD drives working then not working, then I tear the machine apart, put it together, and voila it works only to crap out again. If something is going to be broken, then stay broken.
Some other symptoms with these drives: They "click" sometimes on power-on, and then the system will hang. They will sometimes be recognized in the bios, sometimes not.