Having the same issue here.
Asrock x79 Extreme 4 motherboard
using the ASMEDIA XCHI Controller for USB 3.0
Plug the 3 TB external drive into any of my USB 3.0 ports and the SES device disappears and a USB Mass Storage Device appears appears in conflict (exclamation point).
Plug the drive into any USB 2.0 port and the drive is recognized normally, SES device appears and everything is hunky dory.
Seems to be somewhat common from what I have seen on the net, but not finding any real solutions. Sent an email into WD support but have not heard back from them yet.
Encountered the problem when I first got it, have since upgraded the firmware but still has the same issue.