Windows 7 - intermittent bios hard drive detection

Working on my friends desktop computer and the BIOS doesnt detect the haddrive all the time. If i cold boot or reset the machine the harddrive is not detected. However if i pull the CMOS battery and power cord then drain the capacitors (by pressing the power button) and replug the power the drive is detected by the BIOS and starts booting windows (then freezes). The Computer can boot from CDs fine (from IDE cd drives). when i power up the machine without draining all of it's power/ removing the power cord the BIOS gets stuck detecting the SATA drive.

I tried the Hard drive in my machine it and worked fine so i dont think its a drive/cable problem. i also tried one of my known good WD drives in the machine and it doesnt detect it.

i have tried replacing the signal cable

default settings (no options for IDE/AHCI just enable or disable SATA)

i'm not sure if windows freezing is a 2nd problem or part of the first.

Motherboard: Gigabyte GA-k9ns Version F9
Drive: seagate 500gb sata (also tried a WD green 500gb & black 1TB)

thank you for any tips

Check the hard drive with the manufacturer's diagnostic tools.
Hard Drive Diagnostics Tools and Utilities (Storage) - TACKtech Corp.
HD Diagnostic

Did you try using different SATA sockets on the mobo? Also check if GigaByte has a BIOS update, that may be relevant.
Sometimes you may have to enable SATA/RAID in order to get SATA properly detected, if available.

If you have a IDE/SATA convertor/adapter you could try sorting out whether it is the SATA bus that is acting up. Any warranty left on the board?

have used both drives in both sockets with same results. i have no way to get a floppy to update the bios or to start windows and run their .exe updater.

the BIOS only has an option to enable/disable the SATA bus no RAID option.
I have decided either the SATA is messed up (southbridge or some other chip in between SATA port and southbridge) or the BIOS is corrupted because the machine doesnt even get out of attempting to detect the SATA

Yeah, that would probably be my conclusion as well. Look closely for any defects on the mobo such as scorch marks on condensators or scratches.

Just out of curiosity, have you checked that the power cable to the drive is securely connected?

Do you have a straight PSU-to-SATA cable to the drive, or is it a PSU-to-MOLEX (4-pin) connector and then a short MOLEX-to-SATA adapter to the drive? I had an intermittent drive problem for a year (and even bought a replacement drive, because I thought it was the drive), and tried lots of different things to fix it. Turns out it was the little 3" MOLEX-to-SATA power cable adapter which was at fault, and was occasionally just falling loose and that was the end of 12V power to the drive!

Have you tried an alternate power cable from the PSU to the drive?

Have you tried a different SATA cable from drive to mobo?

Just tossing out ideas.