I have a Sabertooth x58 motherboard and a raptor 300gb drive and a samsung spinpoint F3 1TB HDD, If I put the raptor in the 6 gbp/s port and the 1TB in the 3gb port, the raptor isnt recognised and is not shown in BIOS, only the 1TB.
If I swapped them around so the 1TB is on the 6gbp/s and the raptor is on the 3gb sata port the bios sees it fine and it works ok,
Why cant my velociraptor been seen when plugged into the 6gb sata port? but the samsung tb drive can?
I also have the Sabertooth X58, and recently had the same issue after my Western Digital 10K rpm drive died. Apparently the 3gb port doesn't work with high speed drives. The 6gb ports, otherwise known as "Marvell" ports are setup to be the default HDD ports with the 3gb use for DVD/CD, floppies, RAID configurations, etc...
My 1TB Seagate (brand new out of the box) would not be recognised in the 3gb port, only in the Marvell port would it work. And Windows 7 pro 64 bit wouldn't recognise it until it was partitioned.
One tidbit of info, magnetic (spindle) drives are favored by default to be your boot drive according to Asus tech support. I have an SSD drive as my primary boot drive so I had to manually set the Bios to boot from it.
Hope that helps!