How to fix "512 bytes per sector" to "4096 bytes per sector" for an "Advanced Format" 4K sector USB hard drive?
I had this same issue.  I finally resolved it by connecting to the drive using eSATA instead of USB or Firewire.  My USB/FW enclosure has an eSATA port on the back, and I connected to that instead of USB.  Bypassing the USB circuit in the external enclosure allowed Mac Disk Utility to directly recognize the WD30EZRX 3.0 TB drive, and to partition it correctly to that size.

Luckily I have an older Macbook Pro with and Express/34 slot and an eSATA adapter for that.  I don't know how we are going fix this with newer MacBooks.  Perhaps newer USB interfaces can correctly represent the Advanced Format sector info.