I consistently lose one of my two SATA drives (one SSD, one HD) after (almost?) exactly one hour. Doesn't matter if the computer is at idle or the disk is being written to frequently. The machine is dual boot and the behavior is the same in Windows 7 and Ubuntu 10. Seems to be whichever port is closest to the top of the machine. The drive will disappear and will not remount until I do a hard (power cycling) reboot. Both drives appear to be fine.
I don't see anything in the BIOS that would do this, but 15 times in a row at between 58 and 62 minutes (maybe exactly 60) is some setting somewhere, isn't it? It's an ASUS mobo, AMI BIOS, Marvell controller for the 6GB port, but the phenomenon also happens when both drives are plugged into 3GB/s ports.