Do a basic thing...remove all your peripheral components..remove all the optical drives,ur hard drives etc and just keep one of ur HDD(whichever has OS in it) and start the system.
By removing peripherals i mean CD/DVD/Floppy/Graphics Card(run it on ur Mobo VGA)/LAn Card/Modem/USB Devices etc ....everything thats not critical for booting..
go to BIOS and check if your HDD is detected properly.
have u tried changin the SATA cables??
Once my 250GB drive gave me errors,used to get detected once a while,i changed the cable,and it solved it completely.
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