Borked SATA channels - help!?

I've started having trouble with HDD bays 3 and 4 in my early-08 Pro (3GHz, 8800GT, 4GB RAM).
I first noticed it a few weeks ago - my TimeMachine partition was on a HDD in bay 4, and the backup occasionally failed.
Then the computer started not rebooting (gray screen before the Apple first appears).
Then it started not booting at all.
The stage it fails on booting is very early - before even being able to select which partition to boot from (or even from DVD): gray screen, blank, before the Apple logo or spinner.
So... I tried shuffling the HDDs around thinking one was failing. It doesn't matter which HDD I put in, what DOES matter is that bays 3 and 4 must be empty. If either is occupied, it won't boot.
It also seems to vary slightly with heat: if the machine is cold, it will sometimes let me boot with bays 3 or 4 occupied.
I've tried resetting PRAM, and disconnecting all cables etc. etc. This seems to have no effect.
I also tried plugging a drive into one of the spare SATA lines on the board (a pain to get power to it, but that's another matter). It worked fine.
Since SATA channels seem to work in pairs, this makes me think that this is a chipset problem. I've checked temperatures and they are normal (30°C processors, 36°C northbridge, 45°-50°C RAM).
I wonder whether this might be a firmware issue (IIRC it was updated shortly before the problems appeared). I'm currently on Boot ROM Version MP31.006C.B05 and SMC Version 1.25f4.
Otherwise (sigh) will I have to take this to my 5-week-wait local Apple dealer?

it was the mobo - it was replaced by Apple Service and all is now fine

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George,
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Sincerely,
Technical Support
Technical Support Division
MSI Computer Corp.
http://www.msicomputer.com
MSI - Beyond Expectations!
1-626-913-0828
1-626-581-7721 Fax
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This topic has been moved to Intel P4/Celeron boards.
https://forum-en.msi.com/index.php?topic=142931.0

Nope. Didn't work.
I can try things all day but this doesn't make sense. Surely someone knows what bios settings are required (especially on the MSI board site) to set the bios on a MSI 945p platnium motherboard. I have the sata drive plugged into the Sata 1 connector and bios still says it is ide channel 4 master. The computer will boot with just the sata drive plugged in but the problems start when I plug the ide drives in on ide 1 or 2 or 3.

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(c) 2002-2005 Promise Technology, Inc. All rights reserved.
ID MODE SIZE TRACK-MAPPING STSTUS
========================================================
1 * 1+0 Stripe 300090M 36483/255/63 Functional
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Win2000 Promise FastTrack 376 Itm) Controller <=== I used this one
WinNT Promise FastTrack 376 Itm) Controller
The contents of the floppy disk are :
A:\>dir
Directory of A:\
12/12/2002 03:06 1,536 README.TXT
29/08/2002 09:52 1,100 txtsetup.oem
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3 File(s) 2,648 bytes
1 Dir(s) 1,307,648 bytes free
A:\>dir Win2000
Directory of A:\Win2000
21/01/2006 23:19 <DIR> .
21/01/2006 23:19 <DIR> ..
01/06/2002 01:51 17 Fasttx2k.cat
02/01/2003 20:31 1,960 fasttx2k.INF
18/12/2002 11:15 142,910 fasttx2k.sys
3 File(s) 144,887 bytes
2 Dir(s) 1,307,648 bytes free
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Nope. Didn't work.
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