I seem to have the same problem as countless other people, and I seem to have stumbled upon what it is causing it.
For some odd reason, after I had formatted the MBE 2 TB with the WD Quick Formatter, the symptoms of USB 3.0 being not recognized arose. After doing every fixes that were posted on the forum, I remembered that before I used the WD Quick Formatter, the external drive started without the USB problem right away - and it also powered off it’s own disk spin after being disconnected safely using the Windows 7 “Safely Remove” function in the quicktray.
Thus to test my theory, I opened up a new 2 tb external I had, and hooked it up - which recognized the drive right away without the problematic USB 3.0 yellow box popping up. Did it multiple times to make sure, and everytime I reconnected (even after a full restart), the 2 TB My Book Essential that had not been formatted worked without a problem.
That being said, I believe something must be overwritten during the format process that is causing this problem. I don’t think it’s isolated to my 2 drives, since my preivous 2TB before I RMA-ed for the new one (due to SMART error) also did not recognize USB 3 after a format.
Could anyone chime in as to why this might be happening after a format? and is it possible to restore an already formatted drive to a similar state before the format?