Maybe I missed it in the instructions!
I will suggest anyway that the warning that is given (AFTER) installing SAMBA be put in https://www.ghielectronics.com/support/netmf/sdk/19/netmf-and-gadgeteer-package-2014-r2 text.
C:\Program Files (x86)\Atmel\sam-ba_2.12\doc\usb_notice.html
In order to be able to use a new USB driver, any previously installed driver (e.g. sam-ba v2.10) will not work and the old driver (atm6124.sys) can not be updated to the necessary functionality of new driver. An old driver has to be removed before you can install the new USB driver.
As in doing a ‘repair’ it will hang forever and gives no error…