On the old system:
I first installed the updated AMD chip sets, one of which was labeled an AHCI driver.. something to do with either the southbridge or northbridge controller driver. made no difference.
Then I enabled the AHCI feature in the BIOS.... from IDE to AHCI.
Windows booted up fine for a few reboots.. as I said maybe 5 maybe more, but I only had one issue with no boot media found with the eSATA drive connected at bootup time.
I disconnected the eSATA cable, and windows booted up fine for the next few starts.
Then I got the same no media boot error after POST, and no booting at all.
Finally disconnected all internal drives(as the BIOS wanted to boot from the eSATA drive and then others) and Windows started to boot, but locked up where the windows logo starts to form.
After multiple attempts and attempts at repairing Windows, I then loaded Win7 again onto the spare 250G drive to try to recover the older installation and files and stuff.. thinking I recovered as much data as i needed.. except the vital business emails!... DOH!... and reformatted the larger faster 1Tb drive.. readying it for the new install of Windows(which I've been meaning to do for a while since I uninstalled a few programs and stuff a while back).
I'll do a bit more checking of what drivers each drive is using, and so far all I know about the system is that it has 6 SATA controllers.. no idea on what drivers/chipsets and how many of each are in use, or being used.
First thing I thought was to rearrange the drives onto different ports to see if there's any difference in speeds too.