My second hard drive (SATA) disappears from the system intermittently. I am running XP SP2. The event viewer confirms this stating Maxtor (id #) has disappered from the system. If I restart the system the drive will not reappear; I have to shut down and start the system. As I said it is completely intermittent NO ryhme or reason. I have replaced both cables, power and sata. My OS runs on the primary SATA and the 2nd SATA is the drive that disappears.
 
System specs
MB---ASUS P5KC
2 SATA hard drives Maxtor 80 GB
1 IDE drive WD 80GB

I had the same problem have an asus mobo with a SATA and a 500 gig SATA II drive.  The Sata drive is fine while the SATA II will appear and disappear and often failed during file transfers etc.
 
I tried everything from updating the bios firmware to sata drivers in windows and nothing worked.  I even found that partition magic etc in dos mode would also crash trying to use the drive.  I thought partitioning it to under 137 gig might work, but didnt
 
In the end as a last resort I bought a SATA II card and the moment I installed it the drive has worked flawlessly.
 
In the end I believe that for some reason the asus sata firmware is incompatible with certain sata II drives.  I think unless Asus come up with a firmware fix the only solution is to buy an additional SATA II card.