Maybe I have a solution for you; i faced a similar problem with an ASUS P4S8X-mobo.
I bought an additional PCI 2x SATA 1x PATA controller card 1 yr ago, which I initally couldn't use to boot my hdds directly. I reverted back to an IDE/SATA converter, which works fine (serach for DELOC PCI SATA converter).
Since I was experiencing a lot of disk errors listings in my eventlog (running on XP SP3) recently, I dug into the issue once again.
Here's what I did (after some research on the net):
As various versions of the bios-mod utility CBROM didn't seem to work on ASUS bios files (those contain interally lha-packed system files) I found a reference to a enhanced award bios editor tool (open source) on a russion site, which seem to have been improved not do scramble the original boot files.
award_bios_re.zip (Size: 373.86 KB / Downloads: 29)
With this tool (simple windows interface), you can add your via-rom file to the mobo bios file (I ignored massages stating that the file I was opening didn't seem to be a original bios file; the programm still reads all data; you can even extract files locally).
After that, you need eihter the asus flash utility "aflash" (look on the asus site unter you mobo to be sure to get the correct one) or the windows-base asus update utility. This works from within windows, whereas aflash needs a (dos) bootable disk, which you have to set up first and then you have to copy the flash tool this disk.
As precaution, first back up your mobo-bios to file, then use a copy of this file to apply the bios mod via award bios editor tool.
The window tool can read the mobo bios and save it, read bios info and so on, lastly it also can be used to update the bios from file. Now that's when the modified bios file with the additional pci (?boot?) rom must be used.
When you boot your pc, call up the bios setup (usually <DEL> key on ASUS mobos) and check the boot sequence. If there is an entry called "SCSI/ATA onboard ..." as an additonal option, you hit gold; otherwise, I don't know how the mobo bios will try to read the added pci-rom file (at least that's what happend when I didn't activate this option).
If you can set this option, save your modifications, power down , plug in your SATA-disks to the pci-sata controller, power up again and see if you get a system message from the controller card, seaching for hdds. If so, I bet you will get your system back up running.
Then look for the via raid utility software package, so you can check your sata devices or set up a raid configuration if required
I would have attached all files mentined above, but they're too large, so I settled for the bios editor, as that's not found easily and is the most important utility you need.
Good luck; if you're successful, it would be nice to let me know.
EDIT: added Bios-File, enhanced by VIA-rom file
1014.004.awd.zip (Size: 193.3 KB / Downloads: 16)