If the disks can be detected by the onboard SATA controller that means the connection between the midplane and backplane is OK. I'd first check the cable between your RAID controller and the midplane. Also check the HDD compatibility with your RAID controller. Test the RAID card, cable and HDDs on a different system if possible.
Personally I have tried several Intel RAID controllers on this platform without any issues. I haven't tried Adaptec 5405 myself though, but since it's on the tested hardware list it should be able to work.
we received a replacement mid and backplane and put them in and the disks are now seen on the Adaptec, we are on the most recent BIOS - we were also looking to use a hardware Raid 1 controller to avoid having to install sofware drivers so the OS would be on a hot swap mirror which we have used on many of our servers.
. This is the EZRaid controller from Arcoide - http://www.arcoide.com/product.aspx?PageId=260
But it has the same problem of not seeing the disks through the mid/backplane. Is this truly not a passive backplane?