Hard Drive Errors - I have no idea what to do!!

Motherboard: Gigabyte GA-965P-DS4
HardDrives (all SATA2)
- Samsung HD 103SJ (1TB)
- WDC WD2500KS-00MJB0 (250GB) - Has Windows XP install
- WDC WD500AAKS-00YGA0 (500GB) - Has Windows 7 install
- WDC WD6400AAKS-00A7B2 (640GB)

First thing to say, is this system was working for about 2 months after I bought and installed Windows 7.

Then during DOS/Startup, the computer stopped recognising one or two hard drives - they wouldn't come up during bootphase. However when I got into windows (usually it was the W7 install HDD that disappeared and so I often booted off W7) I would be able to explore the "missing" hdd through windows explorer (it would appear as normal in my computer).

I tried changing which of the 6 Sata2 ports were being used. I changed the Sata wires. I checked everything was plugged in. The problem continued.

Now its mainly the windows 7 (500GB) drive which dissapears, but when it does appear and I try to boot off of it I get
"BOOTMGR is missing"

I booted to XP and ran a search through the windows 7 HDD and sure as anything:
bootmgr exists in
H:\Windows\Boot\PCAT
and
H:\Windows\winsxs\x86_microsoft-windows-b..re-bootmanager-pcat_31bf3856ad364e35_6.1.7600.16385_none_c30008a71484187b

Help - please - is my mobo screwed? or is it the HDDs? or is it a fixable problem!!

You've done everything I would have checked so far (re-seat cables, changed the ports used, found the HDDs in windows). Have you thought about updating or re-flashing your BIOS? Since windows sees the HDDs when the board doesn't, the BIOS may be corrupted. If re-flashing or updating, doesn't solve the issue, I'd think about a new board.

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Not, thats mean that could be something wrong with your Win 7 OS. Not necessarily with the mobo or the HDD.