I've just installed a third hard drive in my system. My motherboard is an Asus A8N-SLI Premium. All the drives are Western Digital and are attached to the nVidia SATA controller not the Silicon Image Raid controller.
A 74GB Raptor on the 1st port with partitions C and D
A 320GB Caviar on the 2nd port with partitions E through J
A Plextor burner on the 3rd port
And I just added the 500GB Caviar to the 4th port with partition K
In my BIOS the hard drives are shown in the order they are attached. For some reason though, in every software tool (Partition Magic, Western Digital Diagnostics, Western Digital Data Lifeguard Tools and XP's built in hard drive management) the new drive which is attached at port 4 shows up as the first drive on the list, before my boot drive.
I suppose it's not a big deal since everything "works" as it should but I am curious as to why the drives show up in that order.
it could just be some sort of glitch. but it doesn't really matter like you said. after all, on my computer, windows (windows, program files, documents and setting) installed into my D: partition but the system boot files (boot.ini, autoexec.bat, config.sys, ntldr, ect) are in the C: partition