I've got a problem with a WD Velociraptor 600 vanishing now and then (during normal operation and while the Os is running), when connected to the Marvell Sata 6G controller of my Motherboard. It doesn't, instead, when connected to the onboard 3G one (ICH10r)
Full system specs: Windows 7 64 on Xeon W3690, 24gb ddr3, Motherboard Asus Rampage III Extreme, HDD1 = PCI Revodrive 2, HDD2 = WD Velociraptor 600.
Do you have the bios storage configuration set to AHCI? I know a lot of people are not happy with the Marvell controller but it is usually when a SSD is connected to that controller. Have you tried changing the sata cable and the sata power cable and making sure you are using the sata3 cable that came with the MB. Is the Velociraptor the only other hdd (besides the Revo) ? You could have a defective controller chip. I don't know if you want to go this route but you could get an add on card with sata3 ports on it and bypass the Marvell chip altogether.
The difference between 3Gbps and 6Gbps will only show up in the burst rate, if at all. There will be no difference in the sustained data transfer rate since the drive will just barely saturate a 1.5Gbps interface.