I have a similar problem: I recently installed a new mobo (Gigabyte Z68X-UD3H). When I connected my HD103SJ first (to the SATA3 port) I almost got a heart attack, my drive did not spin up, BIOS did not recognize it and I had no backup of my data of 6 years... After the third or fourth restart, it was recognized by the BIOS and I boot up from my SSD. I checked HDD Sentinel (disk monitor tool) and it showed, that the condition of the drive is 0% (previously was as always 100%) and advised to save my data since the drive has hardware problems. I saved all my data via USB2.0 (took ages) to an external drive.
I was about to return the mobo to the vendor but suddenly I gave a try to hook the drive up to the SATA2 port and it worked perfectly.... I was looking for this problem but I only found a known error of P67 chipsets (B0 stepping) with SATA2 but not with Z68 chipset and SATA3... I bought two brand new HDDs, HD502HJ (SATA2, 500GB) and WD5000AAKX (SATA3, 500GB) and they all work fine with all possible SATA ports... So I came to a conclusion that my new mobo does not "like" my old HDD...
Core i5-2500k, GB Z68X-UD3H, 2x2GB Kingston Hyper-X Blu XMP, 1TB HDD, MSI R6870 OC, Zalman 500W.