I did not have this issue when I originally installed ISSM. Are you using Windows 8 or 8.1? Please remember that only Windows 8.1 is supported.
As I mentioned I did not have issues the first time I installed ISSM on my PC (Windows 7) but I have gotten access to a Windows 8.1 PC. Let me download and install the software and update you.
Did you make sure to flash the D2000's ROM after installing ISSM? If so, did you have any issue? Or did everything worked as expected? In case you haven't flashed the board's ROM I'd suggest you to do it. You can flash the MCU's ROM in Intel ISSM > Update Target ROM...
Also, make sure the drivers of the board are installed. If you are having issues when trying to debug the board. Should re-install the driver's by running install.bat found in C:\IntelSWTools\ISSM_2016.0.027\debugger\driver.
Those were the steps I did to run the "hello, world" example and I did not have any issues on Windows 8.1.
Let me know if this information is of help for you.
i flashed the D2000's ROM without problem, the problem is building the projetc.
i looked in the foum and found a thread with the exact same problem Fatal error: can't create ../drivers/debug/quark_d2000/obj/qm_adc.o: No such file or directory even the problem iniciating the ISSM, but i get a via message with JON J K (Intel) that give me a new bat to start the ISSM ( https://software.intel.com/en-us/file/testtxt-14/download?token=Z6k1733e ) so i dont know if is something with the SO or the ISSM
Did you make sure to install the latest version of the JRE? In case you didn't you can find it in Download Free Java Software
If the issue persists after installing Java, I'd like to ask you if you have access to another PC to see if this behavior can be replicated.