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Sorry to raise an old thread, but I'm having the same problems on the same machine as you guys. Mid 2009 13.3 MBP.

I've replaced the hard drive cable today, and still nothing... I've ordered a caddy to replace the optical disk drive so I can use my SSD with that connection instead, as the machine is still good when booted via USB.

I'm guessing the same, the SATA port on the logic board for the HDD has gone kaput... do we know if this is a widespread issue?

Same exact problem here on macbook pro 2012
Replaced the optical drive with a caddy, so I'm guessing the hdd sata port on the logic board has failed and changing the logic board is the more expensive solution?
 
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