Clean windows 7 pro install won't detect non-boot SATA drives even though BIOS shows it / them

Having successfully RAID0ed my two SSDs, and was about to RAID0 2 x 2TB SATA Baracudas - the whole install was promptly scrambled after a registry defrag and reboot (from Glary utilities - I think that's what popped it anyway).

After nine hours trying to repair/repeat the RAID0 install I decided to follow the KISS principle (KEEP IT SIMPLE STUPID) - by trying to revert back to two plain SATA SSDs with two SATA HDDs (which was working OK previous to the unsuccessful RAID attempt).

Unfortunately, in the process, once I re-connected HDDs to SATA ports 3 and 4, I can't get windoze (Pro x64) to recognise the HDDs even though they show in the post, the BIOS can see them, the SSDs, and the CD/DVD drive - and the ports are SATA configured in the BIOS (as are the SSDs which boot OK without either/the HDD(s) plugged).

In fact, I can't boot (using the SSD port 0) once I connect the HDD(s either or both). The boot posts then just hangs on a black screen with flashing cursor. If I unplug the HDD(s) then I _can_ boot and see the boot SSD and the second one.

I've tried the windoze install repair boot option but it says something like the version of windows is not appropriate for this device (but it was before and I've only got one (completely kosher) windoze 7 Pro install disk!).

I have backed up some data (drivers and other data backups, Hah!) on the HDDs so don't want try to reformat them if I can help it. Both were formatted in the previous configuration on this rig.

'Any leads for this frustrating problem? Is it possibly to do with having two SATA controllers on the board? Would swapping the ports around make any difference? Please help.

Mobo: ASUS M5A99X EVO (with up-to-date BIOS), 2 x 128GB OCZ Vertex 4s , 2 x ?STDM0001? Baracudas 2TB, SATA DVD/CD
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More about clean windows pro install detect boot sata drives bios shows
  1. check to see if you have a master boot record virus or a damaged boot record on one of the hard drives. with each ssd make sure they have the newest firmware and do a secure erase. on the hard drive check there firmwares and use a 3 party tool to do a contemplate wipe of the drive and master boot record. when you do your install of the sata ssd make sure you do a custom driver install and have the newest amd chipset and raid drivers on a disk or usb stick. if you want save yourself some time slipstream the drivers and windows 7 sp1.
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