I had one more thought, which might just solve your problem.
In the arduino 1.6.6 there is a file "genuino.inf" containing the following two lines:
These lines are not present in the arduino 1.6.5 drivers directory.
So it may be that the genuino zero has different PID values than the arduino zero. The 1.6.6 did not include the edbg in this, I don't know why, so someone more aware of USB drivers and the genuino may have to answer the question. Since 1.6.6 dates only from earlier this month, it may be that 1.6.6 was shipped without being tested on the genuino zero.
In simple terms, you may be able to get the drivers for the native USB port to work for you. It is just as good as the edbg port for developing under the arduino ide.
You might want to look at the arduino software daily build to see if support for the edbg port has been added to the genuino.inf file.
I do want to commend you for being a pioneer adopter of this product, I expect arduino.cc will resolve the issue soon. Keep up your good work.