I have set up a RAID-1 with two identical harddisks WD VelociRaptor WD 3000HLHX-01JJPV0 on an onboard Z77 controller.
Intel Rapid Storage application reports drive 0 running at 3Gb/s and drive 1 at 6Gb/s.
Is here a jumper between 5&6 (I beleive) on the sata2 drive?
if not then try a new cable. rebooting also sometimes helps.
Its a failure of the dive and motherbd to auto-negotiate the sata3 speeds and it falls back to sata2.
I would still consider getting higher quality sata cables. Since the jumper is definitely not on (it switched back to sata3) then the problem is in the signaling.