I have uninstalled RST altogether in the hopes that it might be the source of the issues, and notice a slightly less responsive machine, but give the not-in-BIOS issue, I'm not too optimistic about getting through the day.
Yes, it's that drive. According to folks on the Seagate forums, the specific sub-optimal readings I got are apparently "not generally necessarily" indicative of a true issue. Even if it is the drive, that doesn't explain why the DVD drive on port 0 was disappearing. As the drive hadn't disappeared since I uninstalled RST (7 hours of straight use now), I attempted to the Dell Support Center and see what happens, and the X-Drive (Port 3) disappeared again. I was able to run a diagnostic on the DVD drive without incident.
More good news (sarcasm). After the most recent DSC test, I shut down my computer completely.15 minutes later, when I went to reboot... nothing! The Dell logo on the front lit up, but nothing else. the power button on top (white when on, flashing white when in sleep mode, amber sometimes) was black. I unplugged, replugged. Nothing. Unplugged, went aware in a stupor for 20 minutes contemplating why I did this to myself (the work I'd been doing all day I saved to the C-drive thinking that if the X-drive disappeared I'd still have my work), replugged, booted up. Whew, but I lost a few weeks of my live in stress there.
Osprey's offered some good suggestions.
It could be something board-based (ie: intermittently bad SATA controller, or a simple BIOS update needed).
Could also be one of the drives choking the others.
Obviously you could try booting/running the system with individual (non-system) drives disconnected from SATA/power if the problem is predictable enough.
ie: Trying running with Port 2 disabled/disconnected to verify function. Rinse, repeat w/the other two ports.
It could be the board, or it could be any of the drives flaking out - even if diagnostics suggest they're all fine.
I ran 32-bit diagnostic, and the offending drive twice failed then froze due to IRQ failure. I have since replaced the offending drive (the floods in Thailand have caused a drive shortage and prices are sky high--ouch). In limited hours of usage, there have been no further issues. Fingers crossed. RST is reinstalled. Dell Support Center runs without detaching any drives, and the new drive passes all tests. When transferring files from the old drive to the new, things were going swimmingly until I allowed a brief amount of idleness; then, some background process kicked in (I could hear drives spinning up/heads flying, whatever) and the drive detached. I shut down (to end the flow of power to the MOBO that seems to prevent the drive from reappearing in the bios on a simple restart) and restarted in SAFE MODE. From then on, it was all easy sailing.
I just saw that my Hard Drive Activity Light flashes white. It has only been amber as far as I can remember. ANY documentation on THAT feature (which I assume indicates some type of issue with a hard drive), would have been useful.