like I said in my first post, windows is installed onto a standalone WD NOT the pair of seagates that are in the RAID array... so that doesn't answer my question.
Hmm. Well, looks like you need some troubleshooting and I'll
try to help but know ahead of time I haven't personally used a P5Q Deluxe myself so don't hold my suggestions or ideas against me.
1st) I have to ask. You obviously have your bios boot settings setup properly so it boots into the WD drive first, right? Adding that second drive could have changed the bios settings.
2nd) If the above is correct, then maybe Windows itself is confused during boot-up. Even though your BIOS is set correctly to boot into the WD drive, if you don't have the Windows Boot Manager installed (can you get to F6? or does it reboot before?) then maybe your motherboard's chipset (either Silicon Image or Marvell - I'm assuming) is getting confused. I've seen it before and I know fix it but we'll get to that later if none of my ideas work.
3rd) If the two idea above don't help you, what kind of RAID are you using? Built-in to the motherboard or is a hardware RAID card?
If it's built into the motherboard (and a Silicon Image or Marvell chipset), you maybe you have the wrong settings or haven't updated your settings. You might need to change around IDE, RAID and ACHI to get it to work. I haven't used the Asus P5Q Deluxe myself, so I don't know what you see or have already set in your bios.
4th) Can you confirm that the new Seagate drive is working properly? I ask because maybe it was DOA.
These are
most of my thoughts that come direct to mind. I have one more interesting idea but I'll ask you after you reply if nothing I asked helped.