PMOD settings are fine.
Actually when you click on FX3-->SPI FLASH then it will download the bootprogrammer code into FX3 and it will enumerate back with VID - 04B4 and PID - 4720. It looks like it is not binding to the driver automatically. So please try binding this driver manually (CyUSB3.inf located in the C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.2\driver\bin\win7\x64).
You can do this by right clicking on the device (in Device Manager) and press "Update Driver". Navigate to the location of CyUSB3.inf.
After doing this, you can hit reset and try to program the SPI FLASH (FX3-->SPI FLASH). Then it should be directly asking you for the .img file.
Please make sure that J101 to 104 are connected between 2 and 3 to successfully program the SPI FLASH.