I think I had a similar problem to this in the past but it resolved with a new motherboard. Earlier this morning when my computer was doing its bi-weekly virus scan the scanner halted on one of my drives, stating that it could not read/write to the disk, and data was lost. Ok, weird, that out of no where this would happen, the drive isn't really used for anything other than mp3 storage and recent downloads, which isn't much considering I've been to busy to really do anything online. Anyway, I go into windows explorer and I get the same weird "read/write" error. So I check Disk Management and the drive isn't there, which tells me that somehow it was dismounted. I reboot and check the BIOS which shows the drive clear as day, even in loading the BIOS the drives comes up. So the computer does see the drive, its just something in Windows that happened last night that is preventing the OS from remounting the drive.
Right now and for the past year the drive has been on a EIDE Chain, as a Slave. The other drives in the system are on a RAID 0 Config.
This configuration has worked fine on my system for I would say at least 12 months. The only thing that has changed in the guts is I added a DVD-R drive three weeks ago, which ironically I was planning to use to back up the drive today.