Yes. I'm having the same exact issue.
I'm running a newer version of the Intel Driver (126.96.36.1993) and the issue still exists.
Also running Vista Ultimate x64
Have 2 WD drives on separate SATA cables, separate Power Cables, etc.
1 is Velociraptor, 1 is 2TB Green
I've RMA'd the drives, even though I doubted that was the issue, and get the exact same problem.
Both drives disappear at the exact same time and come back at the same time.
I also have an Asus x58 Motherboard (Rampage II Extreme)
I'm a little disappointed in hearing you are experiencing this issue with Intel's SSD drive as well, I was hoping converting to SSD's may resolve the issue.
My computer problem seemed to go away for a few months during the summer. Maybe i changed a setting somwhere. Now i installed Windows 7 Ultimate 64bit and the same 'drive disappears' is happening again. If i logon to a game like World of Warcraft and sit at the character screen, the computer will reboot within minutes as soon as the drives disappear.
Anyone else with this issue?
If you're using Velociraptors, try the firmware update discussed here: http://hardforum.com/showthread.php?t=1452275
I was having the problem all the time with the original firmware, but upgraded and been running them in raid 0 since Oct 22 on Win 7 x64 - and so far no issues.