this is a stupid hardware glitch but it is known to cause that exact problem:
Some mobos don't like it if you have 2 of the same thing on one ide controller. Others don't like it if you have differnt things on each controller.
I had this same problem, I could boot off win2k disk install the os and restart just fine. As soon as I shutdown it would never boot again saying it couldn't find the hard drive. So I'd go thought it all over again...
Once I swapped one of the hard drive and one of the cd roms around it worked just peachy and I never had another issue with it...
Sooo try that, put one hd and one cd/dvd one the same cable making the cd slave and see what happens. If they are on the same cable now take one off and make it master on the second controller.
Post back results.
