I recently had a very similar post about my WD SATA2 250 GB drive that I had recently purchased. Here is what I learned from it:
First off, setting SATA 2 drive to SATA 1.5 can cause serious problems with windows XP as per the manufacturers details. I was having the same problem where if I didn't short my 5-6 jumpers, they drive wouldn't be recognized at all, but if I did, windows install could not find it; was a nice lose-lose situatio. The issue with the motherboard wast that it was a kinda older K8V ASUS that predated SATA2.
No matter what I tried I could not get windows to recognize it with my new Windows install disk. Then, I found the windows isntall disk that came with this premade system. It containe specific controller drivers that allowed Windows to see everything and run flawlessly in the first attempt.
So, although you seem to be done with this drive, I urge you to get the controller drivers from the manufacturers and put them on a floppy. Then, like mentioned about, press F6 just as windows first runs off the boot CD. It will allow you to get over that last hump.