Everything you suggested doing I did long time ago. The old hard drives had fresh Windows installs. I formatted them both in the mobile racks and outside, and they booted without problems in and out of the mobile racks. The 160 gig drives and 250 gig drive I tried formatting in the mobile racks, but Windows setup crashed, so I formatted them when they were connected directly to the IDE cable, and they worked, but if I put them in the mobile rack, they just wouldn't work for some reason. BIOS identified them and picked them up, but Windows wouldn't boot. Plugged directly to the IDE cable, they booted with no errors. In the past, I could format the drive in the mobile rack, and never had a problem, but that was in my old machine.
As I said, before and yet again, my hard drives and CD/DVD rom drives are always on different IDE channels, and my hard drives are always set to master, since I never have more than one drive in there at a time, unless I'm moving large chunks of information back and forth. I did forget to mention that my DVD drive is set to master on the second IDE channel. Always has been.
I can rule out a bad Windows install because I attempted various installs and formats several times, and I believe I mentioned that before. Problem persists. 13 and 80 gig drives work in the mobile racks, and I can reformat them to death while in the mobile racks, but I can't do it with any of my 160 gig hard drives or my brand new 250 gig hard drive. The larger drives will only format and boot properly when connected directly to the IDE cable, and there is only one connected at any given time.
I would rather post lengthy posts because that way no one is asking me a question to which I have already provided the answer. Saves time and effort, or at least it's supposed to. Depends if people actually take the time to read the posts.
Not to sound disrespectful, but since I wasn't really getting anywhere with this thread, although some people did try to help, and I am thankful, I decided to take the machine in to get checked out from top to bottom. I gave them a complete list of all the symptoms and also a list of what I tried to do. Chances are they're not gonna pay attention anyway. I didn't know what else to do, aside from dishing out a few hundred bucks for new parts and essentially build another system all over again from scratch, but I don't know if that would do any good, and I don't have the resources to figure out what's going on.
I have a feeling it's the motherboard, but at this point, I don't know if I'm right or wrong. I do know that my hard drives are working fine, mobile racks are working fine, power supply is working fine, memory is working fine. Aside from that, I don't really know anymore.
They said it would take about a week to inspect it. I have a feeling I'm gonna end up having to get another motherboard all over again.