I have a similar drive, WD1002FAEX-00Y9A0, with the same problem. I have a Nforce chipset, but the exact same problem. Randomly it boots up on SATA gen2, but 90% of the time it boots as SATA gen1.
What i found is that the drive firmware and the bios on the motherboard have a problem communicating their connection speed. By default , de drive should work at SATA3 speed but since the board does not support it , then it should work at SATA2; the problem is that it won’t do that all the time because of the speed negociating protocol for SATA devices.
A new firmware with a fixed protocol should do the trick , if WD will ever make a new one.
A fix could be to have a program with which we could force our drives to work only as SATA2 devices not let them negociate the speed automatically.
