Arduino Zero, Atmel EDBG, and Atmel Studio 7

I am using the latest Atmel Studio 7 with genuine Arduino.cc Zero boards. When I moved to Atmel Studio 7 it was required that the EDBG firmware update to version 3.25. Some of my boards upgraded fine but some did not, boards bought at different times. The failure was obvious because the upgrade completed immediately, claiming success, but nothing changed.

One of the failing boards was just purchased this month through Arduino.cc and it's clear from the documentation on the web site that EDBG is a feature of the Zero and so it should just work with Atmel Studio.

Clicking on View -> Available Atmel tools then right clicking on EDBG brings up a choice of four options (on the SAMD21XPLAINED board there were 6) and none of the 4 options is "kit mode settings" which would allow selection of "DGI" mode. Discussions in AVRFREAKS forum suggest this setting. Apparently some of the Arduino Zero board hardware comes with improperly initialized EDBG parts.

The ZERO boards that are not debug-able with Atmel Studio 7 work fine with Atmel Studio 6.2.

Is this a production problem at Arduino.cc or is there a way to completely reset the EDBG. It's probably a fuse problem or something in the Arduino supply chain.