I'm seeing this comment on the iFixit instructions for the late 2009 hard drive replace instructions. Might this explain the problem some are experiencing replacing the drive even with one of the same manufacturer?
One thing Andrew left out here, which I discovered on my own, is that even if you have the temperature sensor connected to the correct pins, you ALSO have to make sure that it is 'oriented' properly.
On the sensor connector (the little head that plugs into the hard drive) I saw a little white dot on one side, which it turns out, indicates that's the 'top'. So on my iMac, you have to make sure when you connect the temp sensor connector with the white dot showing.
Otherwise, I got the 6000 rpm fans.
robert Seith, Jun 5 2011 @ 7:52 AM
Also, from the instructions
Step 10 — Hard Drive
Before disconnecting the thermal sensor cable, take note of its orientation. It is extremely important to reinstall the connector in the right orientation so the fans will not run at full speed.
Disconnect the thermal sensor by pulling its connector away from the side of the hard drive.
During reassembly, be sure that the thermal sensor connector is connected to set of pins closest to the SATA connectors.
http://www.ifixit.com/Guide/iMac-Intel-21-5-Inch-EMC-2308-Hard-Drive-Replacement /1766/1