As you can see in the introductory video in Intel® Quark™ Microcontroller Getting Started on Windows*: Video if the USB driver has a bad installation it might produce issues when trying to flash or debug the board. In that case you should run the script install.bat found in C:\IntelSWTools\ISSM_2016.y.xxx\tools\debugger\driver\.
Have you tried this? Did it make any difference?
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What JTAG debugger are you using ? I see that you are using the default 'd2000_onboard.cfg' configuration file to connect to the board - Can you make sure you use the correct FDTI interface configuration file.
The configuration files for Olimex and Flyswatter are provided ....
bin\openocd.exe -f scripts\interface\ftdi\olimex-arm-usb-ocd-h.cfg -f scripts\board\quark_d2000.cfg
bin\openocd.exe -f scripts\interface\ftdi\flyswatter2.cfg -f scripts\board\quark_d2000.cfg
If you have the correct configuration file , you can also try connecting Digitial Pin 0 to GND , reset the board and try flashing again ....
Also , double chek your configuration ... the image below is one we used sucessfully with Olimex Debugger.
Note : Remove all sleeves from Jumpers J9, J10, J11, J15, J17
Pin 1 – Black – (3.3V)
Pin 3 – Yellow - TRST
Pin 4 – Blue - GND
Pin 5 – White - TDI
Pin 7 – Red - TMS
Pint 9 – Green - TCK
Pin 13 – Orange TDO